13-102801022-C-T

Variant names:

• chr13-102801022-C-T
• rs3809373
• NM_017693.4:c.-207+1501C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017693.4(BIVM):​c.-207+1501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 152,254 control chromosomes in the GnomAD database, including 551 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 0.072 (551 hom., cov: 33)
• Consequence: BIVM NM_017693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIVM	NM_017693.4	c.-207+1501C>T		intron_variant	Intron 1 of 10	ENST00000257336.6	NP_060163.2
BIVM	NM_001159596.2	c.-210+1501C>T		intron_variant	Intron 1 of 8		NP_001153068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIVM	ENST00000257336.6	c.-207+1501C>T		intron_variant	Intron 1 of 10	1	NM_017693.4	ENSP00000257336.1
BIVM-ERCC5	ENST00000639435.1	c.-207+1501C>T		intron_variant	Intron 1 of 24	5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.-672+1501C>T		intron_variant	Intron 1 of 23	5		ENSP00000492684.1

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10925 AN: 152136 Hom.: 541 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0515

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0699

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0720 AC: 10960 AN: 152254 Hom.: 551 Cov.: 33 AF XY: 0.0723 AC XY: 5380 AN XY: 74446

African (AFR) AF: 0.135 AC: 5590 AN: 41540

American (AMR) AF: 0.0386 AC: 590 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3468

East Asian (EAS) AF: 0.101 AC: 522 AN: 5184

South Asian (SAS) AF: 0.0517 AC: 250 AN: 4832

European-Finnish (FIN) AF: 0.0656 AC: 696 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0448 AC: 3044 AN: 68010

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0461 Hom.: 331

Bravo AF: 0.0703

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.73
PromoterAI		-0.0023	Neutral
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: rs3809373; hg19: chr13-103453372;