13-102844409-C-T

Position:

• chr13-102844409-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204425.2(BIVM-ERCC5):​c.1450+4606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,088 control chromosomes in the GnomAD database, including 2,639 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 0.18 (2639 hom., cov: 32)
• Consequence: BIVM-ERCC5 NM_001204425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIVM-ERCC5	NM_001204425.2	c.1450+4606C>T		intron_variant			NP_001191354.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIVM-ERCC5	ENST00000639435.1	c.1450+4606C>T		intron_variant		5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.763+4606C>T		intron_variant		5		ENSP00000492684.1
BIVM-ERCC5	ENST00000638434.1	n.362-9348C>T		intron_variant		5		ENSP00000492455.1
BIVM-ERCC5	ENST00000639118.1	n.362-4709C>T		intron_variant		3		ENSP00000492444.1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27337 AN: 151970 Hom.: 2639 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.180 AC: 27349 AN: 152088 Hom.: 2639 Cov.: 32 AF XY: 0.181 AC XY: 13458 AN XY: 74338

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.187

Alfa AF: 0.173 Hom.: 1069

Bravo AF: 0.190

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.45

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: rs2094258; hg19: chr13-103496759;