Variant 8-64371134-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 0.773 in 152,158 control chromosomes in the GnomAD database, including 45,856 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 0.77 ( 45856 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114

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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 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:

0.773

AC:

117581

AN:

152040

Hom.:

45838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.762

Gnomad AMR

AF:

0.793

Gnomad ASJ

AF:

0.731

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.652

Gnomad FIN

AF:

0.887

Gnomad MID

AF:

0.785

Gnomad NFE

AF:

0.817

Gnomad OTH

AF:

0.777

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

GnomAD4 genome

AF:

0.773

AC:

117642

AN:

152158

Hom.:

45856

Cov.:

AF XY:

0.774

AC XY:

57586

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.703

Gnomad4 AMR

AF:

0.793

Gnomad4 ASJ

AF:

0.731

Gnomad4 EAS

AF:

0.612

Gnomad4 SAS

AF:

0.652

Gnomad4 FIN

AF:

0.887

Gnomad4 NFE

AF:

0.816

Gnomad4 OTH

AF:

0.775

Alfa

AF:

0.801

Hom.:

98513

Bravo

AF:

0.764

Asia WGS

AF:

0.628

AC:

2183

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.7

DANN

Benign

0.52

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