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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-40092120-CACACTGTTGTTACTTG-AA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40092120&ref=CACACTGTTGTTACTTG&alt=AA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40092120,
"ref": "CACACTGTTGTTACTTG",
"alt": "AA",
"effect": "missense_variant,conservative_inframe_deletion",
"transcript": "ENST00000642050.2",
"consequences": [
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln91_Cys96delinsPhe",
"transcript": "NM_000310.4",
"protein_id": "NP_000301.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 306,
"cds_start": 271,
"cds_end": null,
"cds_length": 921,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 2284,
"mane_select": "ENST00000642050.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln91_Cys96delinsPhe",
"transcript": "ENST00000642050.2",
"protein_id": "ENSP00000493153.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 306,
"cds_start": 271,
"cds_end": null,
"cds_length": 921,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 2284,
"mane_select": "NM_000310.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.268_284delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln90_Cys95delinsPhe",
"transcript": "ENST00000433473.8",
"protein_id": "ENSP00000394863.4",
"transcript_support_level": 1,
"aa_start": 90,
"aa_end": null,
"aa_length": 305,
"cds_start": 268,
"cds_end": null,
"cds_length": 918,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000530704.6",
"protein_id": "ENSP00000431655.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.358_374delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln120_Cys125delinsPhe",
"transcript": "ENST00000641471.1",
"protein_id": "ENSP00000493146.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 335,
"cds_start": 358,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 2368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.247_263delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln83_Cys88delinsPhe",
"transcript": "ENST00000641083.1",
"protein_id": "ENSP00000493369.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 322,
"cds_start": 247,
"cds_end": null,
"cds_length": 969,
"cdna_start": 265,
"cdna_end": null,
"cdna_length": 2353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln91_Cys96delinsPhe",
"transcript": "ENST00000641319.1",
"protein_id": "ENSP00000493128.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 301,
"cds_start": 271,
"cds_end": null,
"cds_length": 906,
"cdna_start": 303,
"cdna_end": null,
"cdna_length": 2388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln91_Cys96delinsPhe",
"transcript": "NM_001363695.2",
"protein_id": "NP_001350624.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 282,
"cds_start": 271,
"cds_end": null,
"cds_length": 849,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "QVTTVC",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"conservative_inframe_deletion"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln91_Cys96delinsPhe",
"transcript": "ENST00000439754.6",
"protein_id": "ENSP00000403207.2",
"transcript_support_level": 3,
"aa_start": 91,
"aa_end": null,
"aa_length": 282,
"cds_start": 271,
"cds_end": null,
"cds_length": 849,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 2195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*107_*123delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000372779.9",
"protein_id": "ENSP00000361865.5",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*445_*461delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000526547.2",
"protein_id": "ENSP00000436481.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000529905.5",
"protein_id": "ENSP00000432053.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.508_524delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000641236.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*123_*139delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000641548.1",
"protein_id": "ENSP00000492984.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 507,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*123_*139delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000641691.1",
"protein_id": "ENSP00000492910.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*107_*123delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000372779.9",
"protein_id": "ENSP00000361865.5",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*445_*461delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000526547.2",
"protein_id": "ENSP00000436481.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*123_*139delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000641548.1",
"protein_id": "ENSP00000492984.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
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"feature": null
},
{
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"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.*123_*139delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000641691.1",
"protein_id": "ENSP00000492910.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
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"cdna_start": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.234+262_234+278delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000527311.7",
"protein_id": "ENSP00000436695.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 207,
"cds_start": -4,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.125-2624_125-2608delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "NM_001142604.2",
"protein_id": "NP_001136076.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 203,
"cds_start": -4,
"cds_end": null,
"cds_length": 612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "c.125-2624_125-2608delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000449045.7",
"protein_id": "ENSP00000392293.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 203,
"cds_start": -4,
"cds_end": null,
"cds_length": 612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"hgvs_c": "n.124+4979_124+4995delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": null,
"transcript": "ENST00000641924.1",
"protein_id": "ENSP00000493063.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PPT1",
"gene_hgnc_id": 9325,
"dbsnp": "rs386833638",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.098,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM4,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM4",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000642050.2",
"gene_symbol": "PPT1",
"hgnc_id": 9325,
"effects": [
"missense_variant",
"conservative_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.271_287delCAAGTAACAACAGTGTGinsTT",
"hgvs_p": "p.Gln91_Cys96delinsPhe"
}
],
"clinvar_disease": "Neuronal ceroid lipofuscinosis 1",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Neuronal ceroid lipofuscinosis 1",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}