13-102839742-G-A

Variant names:

• chr13-102839742-G-A
• rs34572873
• NM_017693.4:c.1389G>A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BS1 BS2

The NM_017693.4(BIVM):​c.1389G>A​(p.Gly463Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00932 in 1,614,194 control chromosomes in the GnomAD database, including 123 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0066 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0096 (120 hom.)
• Consequence: BIVM NM_017693.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.29

Genes affected

BIVM (HGNC:16034): (basic, immunoglobulin-like variable motif containing) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

BIVM-ERCC5 (HGNC:43690): (BIVM-ERCC5 readthrough) This locus represents naturally occurring read-through transcription between the neighboring BIVM (basic, immunoglobulin-like variable motif containing) and ERCC5 (excision repair cross-complementing rodent repair deficiency, complementation group 5) genes on chromosome 13. The read-through transcript encodes a fusion protein that shares sequence identity with the products of each individual gene. [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 13-102839742-G-A is Benign according to our data. Variant chr13-102839742-G-A is described in ClinVar as [Benign]. Clinvar id is 783043.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.29 with no splicing effect.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00659 (1003/152302) while in subpopulation SAS AF= 0.0205 (99/4826). AF 95% confidence interval is 0.0172. There are 3 homozygotes in gnomad4. There are 496 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIVM	NM_017693.4	c.1389G>A	p.Gly463Gly	synonymous_variant	Exon 11 of 11	ENST00000257336.6	NP_060163.2
BIVM-ERCC5	NM_001204425.2	c.1389G>A	p.Gly463Gly	synonymous_variant	Exon 9 of 23		NP_001191354.2
BIVM	NM_001159596.2	c.723G>A	p.Gly241Gly	synonymous_variant	Exon 9 of 9		NP_001153068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIVM	ENST00000257336.6	c.1389G>A	p.Gly463Gly	synonymous_variant	Exon 11 of 11	1	NM_017693.4	ENSP00000257336.1
BIVM-ERCC5	ENST00000639435.1	c.1389G>A	p.Gly463Gly	synonymous_variant	Exon 11 of 25	5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.702G>A	p.Gly234Gly	synonymous_variant	Exon 10 of 24	5		ENSP00000492684.1

Frequencies

GnomAD3 genomes AF: 0.00659 AC: 1003 AN: 152184 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00171

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00550

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00406

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00946

Gnomad OTH AF: 0.00525

GnomAD3 exomes AF: 0.00849 AC: 2133 AN: 251364 Hom.: 14 AF XY: 0.00944 AC XY: 1283 AN XY: 135850

Gnomad AFR exome AF: 0.00154

Gnomad AMR exome AF: 0.00474

Gnomad ASJ exome AF: 0.0104

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.0250

Gnomad FIN exome AF: 0.00328

Gnomad NFE exome AF: 0.00826

Gnomad OTH exome AF: 0.0104

GnomAD4 exome AF: 0.00961 AC: 14049 AN: 1461892 Hom.: 120 Cov.: 31 AF XY: 0.0102 AC XY: 7399 AN XY: 727248

Gnomad4 AFR exome AF: 0.00131

Gnomad4 AMR exome AF: 0.00472

Gnomad4 ASJ exome AF: 0.0109

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.0249

Gnomad4 FIN exome AF: 0.00313

Gnomad4 NFE exome AF: 0.00943

Gnomad4 OTH exome AF: 0.0105

GnomAD4 genome AF: 0.00659 AC: 1003 AN: 152302 Hom.: 3 Cov.: 32 AF XY: 0.00666 AC XY: 496 AN XY: 74472

Gnomad4 AFR AF: 0.00171

Gnomad4 AMR AF: 0.00549

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.00406

Gnomad4 NFE AF: 0.00947

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00860 Hom.: 1

Bravo AF: 0.00615

Asia WGS AF: 0.00635 AC: 22 AN: 3478

EpiCase AF: 0.00927

EpiControl AF: 0.00794

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Nov 20, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.5
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34572873; hg19: chr13-103492092; COSMIC: COSV57280823;