13-102845567-T-C

Variant names:

• chr13-102845567-T-C
• rs4150247
• ENST00000639435.1:c.1450+5764T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001204425.2(BIVM-ERCC5):​c.1450+5764T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 155,428 control chromosomes in the GnomAD database, including 784 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.094 (775 hom., cov: 33)
  • Exomes 𝑓: 0.075 (9 hom.)
• Consequence: BIVM-ERCC5 NM_001204425.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.59
• Publications: 4 publications found

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]

ENSG00000305730 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 13-102845567-T-C is Benign according to our data. Variant chr13-102845567-T-C is described in ClinVar as Benign. ClinVar VariationId is 1238248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204425.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIVM-ERCC5	NM_001204425.2		c.1450+5764T>C		intron	N/A	NP_001191354.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIVM-ERCC5	ENST00000639435.1	TSL:5	c.1450+5764T>C		intron	N/A	ENSP00000491742.1
	BIVM-ERCC5	ENST00000639132.1	TSL:5	c.763+5764T>C		intron	N/A	ENSP00000492684.1
	ENSG00000305730	ENST00000812635.1		n.185A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14264 AN: 152130 Hom.: 774 Cov.: 33

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0900

GnomAD4 exome AF: 0.0755 AC: 240 AN: 3180 Hom.: 9 Cov.: 0 AF XY: 0.0795 AC XY: 123 AN XY: 1548

African (AFR) AF: 0.0408 AC: 4 AN: 98

American (AMR) AF: 0.0625 AC: 4 AN: 64

Ashkenazi Jewish (ASJ) AF: 0.0776 AC: 18 AN: 232

East Asian (EAS) AF: 0.00 AC: 0 AN: 696

South Asian (SAS) AF: 0.0606 AC: 4 AN: 66

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AF: 0.0625 AC: 2 AN: 32

European-Non Finnish (NFE) AF: 0.104 AC: 181 AN: 1748

Other (OTH) AF: 0.109 AC: 26 AN: 238

GnomAD4 genome AF: 0.0937 AC: 14265 AN: 152248 Hom.: 775 Cov.: 33 AF XY: 0.0934 AC XY: 6951 AN XY: 74450

African (AFR) AF: 0.0575 AC: 2388 AN: 41550

American (AMR) AF: 0.0715 AC: 1095 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3464

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1496 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8297 AN: 68008

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0368 Hom.: 34

Bravo AF: 0.0878

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		-2.6
PromoterAI		-0.0078	Neutral
Mutation Taster		=300/0	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: rs4150247; hg19: chr13-103497917;