NM_017693.4:c.*965A>G

Variant names:

• chr13-102840830-A-G
• rs2018836
• NM_017693.4:c.*965A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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]

ENSG00000305730 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BIVM	NM_017693.4	c.*965A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000257336.6	NP_060163.2
BIVM	NM_001159596.2	c.*965A>G		3_prime_UTR_variant	Exon 9 of 9		NP_001153068.1
BIVM-ERCC5	NM_001204425.2	c.1450+1027A>G		intron_variant	Intron 9 of 22		NP_001191354.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIVM	ENST00000257336.6	c.*965A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_017693.4	ENSP00000257336.1
BIVM-ERCC5	ENST00000639435.1	c.1450+1027A>G		intron_variant	Intron 11 of 24	5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.763+1027A>G		intron_variant	Intron 10 of 23	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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.674 AC: 27919 AN: 41446

American (AMR) AF: 0.614 AC: 9381 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2667 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3277 AN: 5168

South Asian (SAS) AF: 0.652 AC: 3144 AN: 4822

European-Finnish (FIN) AF: 0.654 AC: 6895 AN: 10548

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47014 AN: 67948

Other (OTH) AF: 0.691 AC: 1456 AN: 2106

Alfa AF: 0.691 Hom.: 54739

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
PhyloP100		0.82
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2018836; hg19: chr13-103493180;