Variant 4-40301616-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 0.718 in 152,124 control chromosomes in the GnomAD database, including 39,219 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 0.72 ( 39219 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82

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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 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:

0.718

AC:

109098

AN:

152006

Hom.:

39198

Cov.:

show subpopulations

Gnomad AFR

AF:

0.693

Gnomad AMI

AF:

0.898

Gnomad AMR

AF:

0.735

Gnomad ASJ

AF:

0.710

Gnomad EAS

AF:

0.644

Gnomad SAS

AF:

0.779

Gnomad FIN

AF:

0.755

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.722

Gnomad OTH

AF:

0.719

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

GnomAD4 genome

AF:

0.718

AC:

109173

AN:

152124

Hom.:

39219

Cov.:

AF XY:

0.720

AC XY:

53559

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.693

Gnomad4 AMR

AF:

0.734

Gnomad4 ASJ

AF:

0.710

Gnomad4 EAS

AF:

0.645

Gnomad4 SAS

AF:

0.778

Gnomad4 FIN

AF:

0.755

Gnomad4 NFE

AF:

0.722

Gnomad4 OTH

AF:

0.721

Alfa

AF:

0.718

Hom.:

83356

Bravo

AF:

0.715

Asia WGS

AF:

0.689

AC:

2397

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.043

DANN

Benign

0.36

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