Genetic Variant BIVM-ERCC5:c.1450+5258G>A (chr13-102845061-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000639435.1(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
ENST00000639435.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.312

Publications

13 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639435.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIVM-ERCC5	NM_001204425.2		c.1450+5258G>A		intron	N/A	NP_001191354.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BIVM-ERCC5	ENST00000639435.1	TSL:5	c.1450+5258G>A	intron	N/A	ENSP00000491742.1
BIVM-ERCC5	ENST00000639132.1	TSL:5	c.763+5258G>A	intron	N/A	ENSP00000492684.1
ENSG00000305730	ENST00000812636.1		n.1509C>T	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.756

AC:

114944

AN:

151952

Hom.:

43778

Cov.:

show subpopulations

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:

AN:

118

Hom.:

Cov.:

AF XY:

0.871

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.781

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.756

AC:

115031

AN:

152070

Hom.:

43814

Cov.:

AF XY:

0.754

AC XY:

56065

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.688

AC:

28530

AN:

41478

American (AMR)

AF:

0.681

AC:

10404

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

2987

AN:

3472

East Asian (EAS)

AF:

0.641

AC:

3308

AN:

5164

South Asian (SAS)

AF:

0.718

AC:

3456

AN:

4814

European-Finnish (FIN)

AF:

0.796

AC:

8421

AN:

10576

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.814

AC:

55341

AN:

67978

Other (OTH)

AF:

0.766

AC:

1617

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1420

2840

4261

5681

7101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.790

Hom.:

61722

Bravo

AF:

0.746

Asia WGS

AF:

0.703

AC:

2447

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.9

(source)

DANN

Benign

0.57

PhyloP100

0.31

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over