Variant rs10995190 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.154 in 152,140 control chromosomes in the GnomAD database, including 1,887 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 0.15 ( 1887 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.209

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

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:

0.154

AC:

23388

AN:

152022

Hom.:

1882

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0219

Gnomad SAS

AF:

0.0855

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.154

AC:

23404

AN:

152140

Hom.:

1887

Cov.:

AF XY:

0.155

AC XY:

11494

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.115

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0220

Gnomad4 SAS

AF:

0.0855

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.147

Hom.:

2764

Bravo

AF:

0.147

Asia WGS

AF:

0.0610

AC:

215

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.8

DANN

Benign

0.65

Splicing

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