13-102839042-C-T

Position:

• chr13-102839042-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.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

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:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BIVM	NM_017693.4	c.1218+303C>T		intron_variant		ENST00000257336.6
BIVM-ERCC5	NM_001204425.2	c.1218+303C>T		intron_variant
BIVM	NM_001159596.2	c.531+303C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BIVM	ENST00000257336.6	c.1218+303C>T		intron_variant		1	NM_017693.4	P1

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.194

Alfa AF: 0.185 Hom.: 687

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

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: rs2281885; hg19: chr13-103491392;