Variant 19-22176638-C-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 0.424 in 151,904 control chromosomes in the GnomAD database, including 14,469 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 ( 14469 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.567

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=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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:

0.424

AC:

64357

AN:

151786

Hom.:

14452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.577

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.432

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.393

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

GnomAD4 genome

AF:

0.424

AC:

64416

AN:

151904

Hom.:

14469

Cov.:

AF XY:

0.424

AC XY:

31448

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.414

Gnomad4 ASJ

AF:

0.432

Gnomad4 EAS

AF:

0.359

Gnomad4 SAS

AF:

0.421

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.353

Gnomad4 OTH

AF:

0.394

Alfa

AF:

0.284

Hom.:

820

Bravo

AF:

0.432

Asia WGS

AF:

0.374

AC:

1298

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

2.9

DANN

Benign

0.50

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