Variant 4-74090655-A-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 0.626 in 151,942 control chromosomes in the GnomAD database, including 29,901 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 0.63 ( 29901 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.968

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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.691 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:

0.626

AC:

95075

AN:

151824

Hom.:

29874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.604

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.623

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.685

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.626

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

GnomAD4 genome

AF:

0.626

AC:

95153

AN:

151942

Hom.:

29901

Cov.:

AF XY:

0.631

AC XY:

46835

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.604

Gnomad4 AMR

AF:

0.703

Gnomad4 ASJ

AF:

0.623

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.685

Gnomad4 NFE

AF:

0.620

Gnomad4 OTH

AF:

0.625

Alfa

AF:

0.617

Hom.:

16074

Bravo

AF:

0.626

Asia WGS

AF:

0.586

AC:

2038

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.87

DANN

Benign

0.56

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