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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: 3-146121108-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=146121108&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 146121108,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000282903.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "NM_182943.3",
"protein_id": "NP_891988.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 758,
"cds_start": -4,
"cds_end": null,
"cds_length": 2277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3749,
"mane_select": "ENST00000282903.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000282903.10",
"protein_id": "ENSP00000282903.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 758,
"cds_start": -4,
"cds_end": null,
"cds_length": 2277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3749,
"mane_select": "NM_182943.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000360060.7",
"protein_id": "ENSP00000353170.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 737,
"cds_start": -4,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703518.1",
"protein_id": "ENSP00000515350.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 758,
"cds_start": -4,
"cds_end": null,
"cds_length": 2277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703522.1",
"protein_id": "ENSP00000515353.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 758,
"cds_start": -4,
"cds_end": null,
"cds_length": 2277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703527.1",
"protein_id": "ENSP00000515355.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 758,
"cds_start": -4,
"cds_end": null,
"cds_length": 2277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "NM_000935.3",
"protein_id": "NP_000926.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 737,
"cds_start": -4,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703523.1",
"protein_id": "ENSP00000515354.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 737,
"cds_start": -4,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.254+4G>A",
"hgvs_p": null,
"transcript": "ENST00000469350.6",
"protein_id": "ENSP00000419963.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 709,
"cds_start": -4,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.173+4G>A",
"hgvs_p": null,
"transcript": "ENST00000494950.5",
"protein_id": "ENSP00000420094.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 703,
"cds_start": -4,
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"cds_length": 2112,
"cdna_start": null,
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"cdna_length": 2908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000706635.1",
"protein_id": "ENSP00000516475.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 702,
"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
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"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 18,
"intron_rank": 3,
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"gene_symbol": "PLOD2",
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"hgvs_c": "c.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000706626.1",
"protein_id": "ENSP00000516472.1",
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"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 16,
"intron_rank": 3,
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"gene_symbol": "PLOD2",
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"hgvs_c": "c.173+4G>A",
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"transcript": "ENST00000703528.1",
"protein_id": "ENSP00000515356.1",
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 21,
"intron_rank": 4,
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"gene_symbol": "PLOD2",
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"hgvs_c": "n.*102+4G>A",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "n.140+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703517.1",
"protein_id": null,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
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"exon_count": 21,
"intron_rank": 4,
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"gene_symbol": "PLOD2",
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"hgvs_c": "n.355+4G>A",
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"transcript": "ENST00000703519.1",
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},
{
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"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 3,
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"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "n.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703520.1",
"protein_id": "ENSP00000515351.1",
"transcript_support_level": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 20,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "n.338+4G>A",
"hgvs_p": null,
"transcript": "ENST00000703521.1",
"protein_id": "ENSP00000515352.1",
"transcript_support_level": null,
"aa_start": null,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 18,
"intron_rank": 3,
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"gene_symbol": "PLOD2",
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"hgvs_c": "n.533+4G>A",
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},
{
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"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 3,
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"hgvs_c": "n.533+4G>A",
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"transcript": "ENST00000703529.1",
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},
{
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"consequences": [
"splice_region_variant",
"intron_variant"
],
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"intron_rank": 3,
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"gene_symbol": "PLOD2",
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"transcript": "ENST00000706627.1",
"protein_id": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"hgvs_c": "n.533+4G>A",
"hgvs_p": null,
"transcript": "ENST00000706634.1",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 3,
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"gene_symbol": "PLOD2",
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{
"aa_ref": null,
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"canonical": false,
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"intron_variant"
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},
{
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},
{
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"intron_variant"
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"gene_symbol": "PLOD2",
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"cdna_length": 2011,
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"feature": null
}
],
"gene_symbol": "PLOD2",
"gene_hgnc_id": 9082,
"dbsnp": "rs4681297",
"frequency_reference_population": 0.76722234,
"hom_count_reference_population": 467888,
"allele_count_reference_population": 1216675,
"gnomad_exomes_af": 0.766137,
"gnomad_genomes_af": 0.777457,
"gnomad_exomes_ac": 1098486,
"gnomad_genomes_ac": 118189,
"gnomad_exomes_homalt": 421869,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.017999999225139618,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.509,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000489901391783687,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000282903.10",
"gene_symbol": "PLOD2",
"hgnc_id": 9082,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.338+4G>A",
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}
],
"clinvar_disease": "Bruck syndrome 2,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|Bruck syndrome 2|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}