Variant rs3825163 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant allele was found at a frequency of 0.000199 in 860,262 control chromosomes in the GnomAD database, including 1 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 0.00036 ( 0 hom., cov: 28)

Exomes 𝑓: 0.00017 ( 1 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.569

Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.000359

AC:

AN:

136560

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000570

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000717

Gnomad ASJ

AF:

0.000302

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0139

Gnomad NFE

AF:

0.000153

Gnomad OTH

AF:

0.00271

GnomAD4 exome

AF:

0.000169

AC:

122

AN:

723630

Hom.:

Cov.:

AF XY:

0.000153

AC XY:

AN XY:

364946

show subpopulations

Gnomad4 AFR exome

AF:

0.000786

Gnomad4 AMR exome

AF:

0.000636

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000319

Gnomad4 SAS exome

AF:

0.0000239

Gnomad4 FIN exome

AF:

0.0000456

Gnomad4 NFE exome

AF:

0.000158

Gnomad4 OTH exome

AF:

0.000240

GnomAD4 genome

AF:

0.000359

AC:

AN:

136632

Hom.:

Cov.:

AF XY:

0.000366

AC XY:

AN XY:

65508

show subpopulations

Gnomad4 AFR

AF:

0.000569

Gnomad4 AMR

AF:

0.000717

Gnomad4 ASJ

AF:

0.000302

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000153

Gnomad4 OTH

AF:

0.00269

Alfa

AF:

0.000248

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over