rs2016073

Positions:

• chr13-102845061-G-A

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+5258G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,188 control chromosomes in the GnomAD database, including 43,854 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 0.76 (43814 hom., cov: 31)
  • Exomes 𝑓: 0.81 (40 hom.)
• Consequence: BIVM-ERCC5 NM_001204425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIVM-ERCC5	NM_001204425.2	c.1450+5258G>A		intron_variant			NP_001191354.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIVM-ERCC5	ENST00000639435.1	c.1450+5258G>A		intron_variant		5		ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	c.763+5258G>A		intron_variant		5		ENSP00000492684.1
BIVM-ERCC5	ENST00000638434.1	n.362-8696G>A		intron_variant		5		ENSP00000492455.1
BIVM-ERCC5	ENST00000639118.1	n.362-4057G>A		intron_variant		3		ENSP00000492444.1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114944 AN: 151952 Hom.: 43778 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.805 AC: 95 AN: 118 Hom.: 40 Cov.: 0 AF XY: 0.871 AC XY: 54 AN XY: 62

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.756 AC: 115031 AN: 152070 Hom.: 43814 Cov.: 31 AF XY: 0.754 AC XY: 56065 AN XY: 74340

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.766

Alfa AF: 0.795 Hom.: 48707

Bravo AF: 0.746

Asia WGS AF: 0.703 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.57

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: rs2016073; hg19: chr13-103497411;