Variant 3-22931621-G-T 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 0.369 in 151,250 control chromosomes in the GnomAD database, including 11,070 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 0.37 ( 11070 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.235

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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:

0.369

AC:

55722

AN:

151132

Hom.:

11044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.428

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.519

Gnomad FIN

AF:

0.279

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.409

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

GnomAD4 genome

AF:

0.369

AC:

55794

AN:

151250

Hom.:

11070

Cov.:

AF XY:

0.374

AC XY:

27661

AN XY:

73912

show subpopulations

Gnomad4 AFR

AF:

0.429

Gnomad4 AMR

AF:

0.500

Gnomad4 ASJ

AF:

0.499

Gnomad4 EAS

AF:

0.533

Gnomad4 SAS

AF:

0.519

Gnomad4 FIN

AF:

0.279

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.407

Alfa

AF:

0.274

Hom.:

1539

Bravo

AF:

0.386

Asia WGS

AF:

0.535

AC:

1855

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.44

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