Variant 21-44989099-C-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 0.181 in 152,188 control chromosomes in the GnomAD database, including 2,641 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 0.18 ( 2641 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 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:

0.181

AC:

27480

AN:

152070

Hom.:

2643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.181

AC:

27485

AN:

152188

Hom.:

2641

Cov.:

AF XY:

0.181

AC XY:

13496

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.134

Gnomad4 AMR

AF:

0.244

Gnomad4 ASJ

AF:

0.239

Gnomad4 EAS

AF:

0.170

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.180

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.103

Hom.:

157

Bravo

AF:

0.186

Asia WGS

AF:

0.158

AC:

550

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.5

DANN

Benign

0.58

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