Variant 21-44985839-G-A 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 0.803 in 152,176 control chromosomes in the GnomAD database, including 49,155 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 0.80 ( 49155 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.70

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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:

0.803

AC:

122091

AN:

152058

Hom.:

49115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.836

Gnomad AMI

AF:

0.750

Gnomad AMR

AF:

0.816

Gnomad ASJ

AF:

0.775

Gnomad EAS

AF:

0.831

Gnomad SAS

AF:

0.824

Gnomad FIN

AF:

0.790

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.801

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

GnomAD4 genome

AF:

0.803

AC:

122190

AN:

152176

Hom.:

49155

Cov.:

AF XY:

0.802

AC XY:

59672

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.836

Gnomad4 AMR

AF:

0.816

Gnomad4 ASJ

AF:

0.775

Gnomad4 EAS

AF:

0.830

Gnomad4 SAS

AF:

0.824

Gnomad4 FIN

AF:

0.790

Gnomad4 NFE

AF:

0.781

Gnomad4 OTH

AF:

0.802

Alfa

AF:

0.795

Hom.:

13689

Bravo

AF:

0.803

Asia WGS

AF:

0.841

AC:

2922

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.40

DANN

Benign

0.43

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