13-102801022-C-T

Position:

• chr13-102801022-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

BIVM (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
BIVM	NM_017693.4	c.-207+1501C>T		intron_variant		ENST00000257336.6	NP_060163.2
BIVM	NM_001159596.2	c.-210+1501C>T		intron_variant			NP_001153068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIVM	ENST00000257336.6	c.-207+1501C>T		intron_variant		1	NM_017693.4	ENSP00000257336.1
BIVM-ERCC5	ENST00000639435.1	c.-207+1501C>T		intron_variant		5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.-672+1501C>T		intron_variant		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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0517

Gnomad4 FIN AF: 0.0656

Gnomad4 NFE AF: 0.0448

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0431 Hom.: 214

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

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: rs3809373; hg19: chr13-103453372;