Variant chr13-102845499-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001204425.2(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
NM_001204425.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.599

Variant links:

Genes affected

BIVM-ERCC5 (HGNC:):

BIVM-ERCC5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BIVM-ERCC5	NM_001204425.2 linkuse as main transcript	c.1450+5696G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.375

Gnomad4 SAS exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.238

GnomAD4 genome

AF:

0.248

AC:

37752

AN:

152064

Hom.:

5407

Cov.:

AF XY:

0.248

AC XY:

18405

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.221

Gnomad4 EAS

AF:

0.397

Gnomad4 SAS

AF:

0.195

Gnomad4 FIN

AF:

0.173

Gnomad4 NFE

AF:

0.172

Gnomad4 OTH

AF:

0.235

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 09, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.2

DANN

Benign

0.46

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over