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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: 12-55694289-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=55694289&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 55694289,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000257879.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2399G>C",
"hgvs_p": "p.Arg800Pro",
"transcript": "NM_002206.3",
"protein_id": "NP_002197.2",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2399,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 2621,
"cdna_end": null,
"cdna_length": 4126,
"mane_select": "ENST00000257879.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2399G>C",
"hgvs_p": "p.Arg800Pro",
"transcript": "ENST00000257879.11",
"protein_id": "ENSP00000257879.7",
"transcript_support_level": 1,
"aa_start": 800,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2399,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 2621,
"cdna_end": null,
"cdna_length": 4126,
"mane_select": "NM_002206.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2411G>C",
"hgvs_p": "p.Arg804Pro",
"transcript": "ENST00000553804.6",
"protein_id": "ENSP00000452120.1",
"transcript_support_level": 1,
"aa_start": 804,
"aa_end": null,
"aa_length": 1141,
"cds_start": 2411,
"cds_end": null,
"cds_length": 3426,
"cdna_start": 2633,
"cdna_end": null,
"cdna_length": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2531G>C",
"hgvs_p": "p.Arg844Pro",
"transcript": "NM_001410977.1",
"protein_id": "NP_001397906.1",
"transcript_support_level": null,
"aa_start": 844,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2531,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2753,
"cdna_end": null,
"cdna_length": 4258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2531G>C",
"hgvs_p": "p.Arg844Pro",
"transcript": "ENST00000555728.5",
"protein_id": "ENSP00000452387.1",
"transcript_support_level": 5,
"aa_start": 844,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2531,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2560,
"cdna_end": null,
"cdna_length": 3930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2411G>C",
"hgvs_p": "p.Arg804Pro",
"transcript": "NM_001144996.2",
"protein_id": "NP_001138468.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1141,
"cds_start": 2411,
"cds_end": null,
"cds_length": 3426,
"cdna_start": 2633,
"cdna_end": null,
"cdna_length": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2393G>C",
"hgvs_p": "p.Arg798Pro",
"transcript": "NM_001414029.1",
"protein_id": "NP_001400958.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 1135,
"cds_start": 2393,
"cds_end": null,
"cds_length": 3408,
"cdna_start": 2615,
"cdna_end": null,
"cdna_length": 4120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2381G>C",
"hgvs_p": "p.Arg794Pro",
"transcript": "NM_001374465.1",
"protein_id": "NP_001361394.1",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 1131,
"cds_start": 2381,
"cds_end": null,
"cds_length": 3396,
"cdna_start": 2603,
"cdna_end": null,
"cdna_length": 4108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2381G>C",
"hgvs_p": "p.Arg794Pro",
"transcript": "ENST00000347027.10",
"protein_id": "ENSP00000343009.6",
"transcript_support_level": 5,
"aa_start": 794,
"aa_end": null,
"aa_length": 1131,
"cds_start": 2381,
"cds_end": null,
"cds_length": 3396,
"cdna_start": 2583,
"cdna_end": null,
"cdna_length": 4084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2411G>C",
"hgvs_p": "p.Arg804Pro",
"transcript": "ENST00000557555.3",
"protein_id": "ENSP00000451039.3",
"transcript_support_level": 5,
"aa_start": 804,
"aa_end": null,
"aa_length": 1122,
"cds_start": 2411,
"cds_end": null,
"cds_length": 3369,
"cdna_start": 2411,
"cdna_end": null,
"cdna_length": 3739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2411G>C",
"hgvs_p": "p.Arg804Pro",
"transcript": "ENST00000691973.1",
"protein_id": "ENSP00000509141.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1117,
"cds_start": 2411,
"cds_end": null,
"cds_length": 3354,
"cdna_start": 2411,
"cdna_end": null,
"cdna_length": 3811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2324G>C",
"hgvs_p": "p.Arg775Pro",
"transcript": "NM_001414030.1",
"protein_id": "NP_001400959.1",
"transcript_support_level": null,
"aa_start": 775,
"aa_end": null,
"aa_length": 1112,
"cds_start": 2324,
"cds_end": null,
"cds_length": 3339,
"cdna_start": 2546,
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"cdna_length": 4051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2312G>C",
"hgvs_p": "p.Arg771Pro",
"transcript": "NM_001414031.1",
"protein_id": "NP_001400960.1",
"transcript_support_level": null,
"aa_start": 771,
"aa_end": null,
"aa_length": 1108,
"cds_start": 2312,
"cds_end": null,
"cds_length": 3327,
"cdna_start": 2534,
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"cdna_length": 4039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2279G>C",
"hgvs_p": "p.Arg760Pro",
"transcript": "NM_001414032.1",
"protein_id": "NP_001400961.1",
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"cds_start": 2279,
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"cdna_start": 2501,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2216G>C",
"hgvs_p": "p.Arg739Pro",
"transcript": "NM_001414033.1",
"protein_id": "NP_001400962.1",
"transcript_support_level": null,
"aa_start": 739,
"aa_end": null,
"aa_length": 1076,
"cds_start": 2216,
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"cds_length": 3231,
"cdna_start": 2438,
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"cdna_length": 3943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2174G>C",
"hgvs_p": "p.Arg725Pro",
"transcript": "NM_001414034.1",
"protein_id": "NP_001400963.1",
"transcript_support_level": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2120G>C",
"hgvs_p": "p.Arg707Pro",
"transcript": "NM_001144997.2",
"protein_id": "NP_001138469.1",
"transcript_support_level": null,
"aa_start": 707,
"aa_end": null,
"aa_length": 1044,
"cds_start": 2120,
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"cdna_start": 2259,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2120G>C",
"hgvs_p": "p.Arg707Pro",
"transcript": "ENST00000452168.6",
"protein_id": "ENSP00000393844.2",
"transcript_support_level": 2,
"aa_start": 707,
"aa_end": null,
"aa_length": 1044,
"cds_start": 2120,
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"cdna_start": 2262,
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"mane_select": null,
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},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
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"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2072G>C",
"hgvs_p": "p.Arg691Pro",
"transcript": "NM_001367993.1",
"protein_id": "NP_001354922.1",
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},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.2060G>C",
"hgvs_p": "p.Arg687Pro",
"transcript": "NM_001414035.1",
"protein_id": "NP_001400964.1",
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"aa_start": 687,
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"cds_start": 2060,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.1925G>C",
"hgvs_p": "p.Arg642Pro",
"transcript": "ENST00000557257.2",
"protein_id": "ENSP00000450578.2",
"transcript_support_level": 4,
"aa_start": 642,
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"aa_length": 979,
"cds_start": 1925,
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"cdna_start": 2041,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"hgvs_c": "c.1055G>C",
"hgvs_p": "p.Arg352Pro",
"transcript": "NM_001367994.1",
"protein_id": "NP_001354923.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 689,
"cds_start": 1055,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2449,
"cdna_end": null,
"cdna_length": 3954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
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"transcript": "ENST00000691052.1",
"protein_id": "ENSP00000508886.1",
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
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"gene_symbol": "ITGA7",
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"hgvs_c": "n.*851G>C",
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"transcript": "ENST00000691846.1",
"protein_id": "ENSP00000508870.1",
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"aa_end": null,
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"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 2700,
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"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITGA7",
"gene_hgnc_id": 6143,
"dbsnp": "rs143929243",
"frequency_reference_population": 0.000005576443,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000547318,
"gnomad_genomes_af": 0.0000065678,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.710167646408081,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.217,
"revel_prediction": "Benign",
"alphamissense_score": 0.667,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.423,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000257879.11",
"gene_symbol": "ITGA7",
"hgnc_id": 6143,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2399G>C",
"hgvs_p": "p.Arg800Pro"
}
],
"clinvar_disease": "Congenital muscular dystrophy due to integrin alpha-7 deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Congenital muscular dystrophy due to integrin alpha-7 deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}