13-102839042-C-T

Variant names:

• chr13-102839042-C-T
• rs2281885
• NM_017693.4:c.1218+303C>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.1218+303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,040 control chromosomes in the GnomAD database, including 2,946 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 0.19 (2946 hom., cov: 32)
• Consequence: BIVM NM_017693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIVM	NM_017693.4	c.1218+303C>T		intron_variant	Intron 10 of 10	ENST00000257336.6	NP_060163.2
BIVM-ERCC5	NM_001204425.2	c.1218+303C>T		intron_variant	Intron 8 of 22		NP_001191354.2
BIVM	NM_001159596.2	c.531+303C>T		intron_variant	Intron 8 of 8		NP_001153068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIVM	ENST00000257336.6	c.1218+303C>T		intron_variant	Intron 10 of 10	1	NM_017693.4	ENSP00000257336.1
BIVM-ERCC5	ENST00000639435.1	c.1218+303C>T		intron_variant	Intron 10 of 24	5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.531+303C>T		intron_variant	Intron 9 of 23	5		ENSP00000492684.1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29212 AN: 151922 Hom.: 2944 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.192 AC: 29234 AN: 152040 Hom.: 2946 Cov.: 32 AF XY: 0.193 AC XY: 14366 AN XY: 74302

African (AFR) AF: 0.196 AC: 8124 AN: 41468

American (AMR) AF: 0.234 AC: 3574 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 709 AN: 3466

East Asian (EAS) AF: 0.361 AC: 1865 AN: 5164

South Asian (SAS) AF: 0.184 AC: 887 AN: 4812

European-Finnish (FIN) AF: 0.171 AC: 1808 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11625 AN: 67972

Other (OTH) AF: 0.194 AC: 409 AN: 2112

Alfa AF: 0.186 Hom.: 702

Bravo AF: 0.204

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.62
PhyloP100		0.025
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: rs2281885; hg19: chr13-103491392;