Variant rs2241107 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 0.358 in 1,559,212 control chromosomes in the GnomAD database, including 104,019 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 0.42 ( 14913 hom., cov: 33)

Exomes 𝑓: 0.35 ( 89106 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.63

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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.420

AC:

63754

AN:

151950

Hom.:

14870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.632

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.289

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.403

GnomAD4 exome

AF:

0.352

AC:

494680

AN:

1407144

Hom.:

89106

Cov.:

AF XY:

0.348

AC XY:

242503

AN XY:

695970

show subpopulations

Gnomad4 AFR exome

AF:

0.651

Gnomad4 AMR exome

AF:

0.297

Gnomad4 ASJ exome

AF:

0.304

Gnomad4 EAS exome

AF:

0.166

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.356

Gnomad4 OTH exome

AF:

0.359

GnomAD4 genome

AF:

0.420

AC:

63845

AN:

152068

Hom.:

14913

Cov.:

AF XY:

0.413

AC XY:

30700

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.633

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.301

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.288

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.357

Gnomad4 OTH

AF:

0.399

Alfa

AF:

0.290

Hom.:

993

Bravo

AF:

0.427

Asia WGS

AF:

0.243

AC:

848

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.36

DANN

Benign

0.60

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