Genetic Variant BIVM-ERCC5:c.1450+5764T>C (chr13-102845567-T-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+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
ENST00000639435.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.59

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=-0.84).

BP6

Variant 13-102845567-T-C is Benign according to our data. Variant chr13-102845567-T-C is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIVM-ERCC5	NM_001204425.2 link	c.1450+5764T>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+5764T>C		intron_variant	Intron 11 of 24	5		ENSP00000491742.1		R4GMW8
BIVM-ERCC5	ENST00000639132.1 link	c.763+5764T>C		intron_variant	Intron 10 of 23	5		ENSP00000492684.1		A0A1W2PS85

Frequencies

GnomAD3 genomes

AF:

0.0938

AC:

14264

AN:

152130

Hom.:

774

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.0795

AC XY:

123

AN XY:

1548

show subpopulations

African (AFR)

AF:

0.0408

AC:

AN:

American (AMR)

AF:

0.0625

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.0776

AC:

AN:

232

East Asian (EAS)

AF:

0.00

AC:

AN:

696

South Asian (SAS)

AF:

0.0606

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AF:

0.0625

AC:

AN:

European-Non Finnish (NFE)

AF:

0.104

AC:

181

AN:

1748

Other (OTH)

AF:

0.109

AC:

AN:

238

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0937

AC:

14265

AN:

152248

Hom.:

775

Cov.:

AF XY:

0.0934

AC XY:

6951

AN XY:

74450

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8297

AN:

68008

Other (OTH)

AF:

0.0881

AC:

186

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

696

1393

2089

2786

3482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0368

Hom.:

Bravo

AF:

0.0878

Asia WGS

AF:

0.0360

AC:

125

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

Jan 10, 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

-0.84

CADD

Benign

1.7

(source)

DANN

Benign

0.33

PhyloP100

-2.6

PromoterAI

-0.0078

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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13-102845567-T-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