Genetic Variant BIVM-ERCC5:c.1450+5696G>C (chr13-102845499-G-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000639435.1(BIVM-ERCC5):c.1450+5696G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,384 control chromosomes in the GnomAD database, including 5,415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5407 hom., cov: 33)

Exomes 𝑓: 0.22 ( 8 hom. )

Consequence

BIVM-ERCC5
ENST00000639435.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.599

Publications

4 publications found

Variant links:

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]

BIVM-ERCC5 links:

ENSG00000305730 (HGNC:):

ENSG00000305730 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 13-102845499-G-C is Benign according to our data. Variant chr13-102845499-G-C is described in ClinVar as [Benign]. Clinvar id is 1242141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIVM-ERCC5	NM_001204425.2 link	c.1450+5696G>C		intron_variant	Intron 9 of 22		NP_001191354.2	R4GMW8Q59FZ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIVM-ERCC5	ENST00000639435.1 link	c.1450+5696G>C		intron_variant	Intron 11 of 24	5		ENSP00000491742.1		R4GMW8
BIVM-ERCC5	ENST00000639132.1 link	c.763+5696G>C		intron_variant	Intron 10 of 23	5		ENSP00000492684.1		A0A1W2PS85

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37715

AN:

151944

Hom.:

5401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.382

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.235

GnomAD4 exome

AF:

0.216

AC:

AN:

320

Hom.:

Cov.:

AF XY:

0.179

AC XY:

AN XY:

184

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

AN:

East Asian (EAS)

AF:

0.375

AC:

AN:

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.161

AC:

AN:

180

Other (OTH)

AF:

0.238

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.248

AC:

37752

AN:

152064

Hom.:

5407

Cov.:

AF XY:

0.248

AC XY:

18405

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.381

AC:

15812

AN:

41450

American (AMR)

AF:

0.255

AC:

3906

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

766

AN:

3466

East Asian (EAS)

AF:

0.397

AC:

2051

AN:

5160

South Asian (SAS)

AF:

0.195

AC:

939

AN:

4820

European-Finnish (FIN)

AF:

0.173

AC:

1829

AN:

10588

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11717

AN:

67972

Other (OTH)

AF:

0.235

AC:

495

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1387

2774

4162

5549

6936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.210

Hom.:

494

Bravo

AF:

0.267

Asia WGS

AF:

0.312

AC:

1085

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 09, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.2

(source)

DANN

Benign

0.46

PhyloP100

-0.60

PromoterAI

0.038

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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13-102845499-G-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over