chr13-102840830-A-G

Position:

• chr13-102840830-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017693.4(BIVM):​c.*965A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,986 control chromosomes in the GnomAD database, including 34,631 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.68 (34631 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: BIVM NM_017693.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIVM	NM_017693.4	c.*965A>G		3_prime_UTR_variant	11/11	ENST00000257336.6	NP_060163.2
BIVM	NM_001159596.2	c.*965A>G		3_prime_UTR_variant	9/9		NP_001153068.1
BIVM-ERCC5	NM_001204425.2	c.1450+1027A>G		intron_variant			NP_001191354.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIVM	ENST00000257336.6	c.*965A>G		3_prime_UTR_variant	11/11	1	NM_017693.4	ENSP00000257336.1
BIVM-ERCC5	ENST00000639435.1	c.1450+1027A>G		intron_variant		5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.763+1027A>G		intron_variant		5		ENSP00000492684.1

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102512 AN: 151866 Hom.: 34584 Cov.: 31

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.687

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.675 AC: 102612 AN: 151984 Hom.: 34631 Cov.: 31 AF XY: 0.673 AC XY: 50006 AN XY: 74302

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.691

Alfa AF: 0.693 Hom.: 43207

Bravo AF: 0.673

Asia WGS AF: 0.678 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.59

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: rs2018836; hg19: chr13-103493180;