Variant rs718768 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 0.751 in 152,196 control chromosomes in the GnomAD database, including 43,310 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 0.75 ( 43310 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0250

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 (EAS) allele frequency at 95% confidence interval = 0.914 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:

0.751

AC:

114212

AN:

152078

Hom.:

43250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.805

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.769

Gnomad ASJ

AF:

0.663

Gnomad EAS

AF:

0.937

Gnomad SAS

AF:

0.778

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.727

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

GnomAD4 genome

AF:

0.751

AC:

114334

AN:

152196

Hom.:

43310

Cov.:

AF XY:

0.754

AC XY:

56120

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.805

Gnomad4 AMR

AF:

0.769

Gnomad4 ASJ

AF:

0.663

Gnomad4 EAS

AF:

0.936

Gnomad4 SAS

AF:

0.778

Gnomad4 FIN

AF:

0.710

Gnomad4 NFE

AF:

0.711

Gnomad4 OTH

AF:

0.730

Alfa

AF:

0.711

Hom.:

49235

Bravo

AF:

0.757

Asia WGS

AF:

0.859

AC:

2985

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

1.9

DANN

Benign

0.43

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