Variant rs6901854 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 0.523 in 152,042 control chromosomes in the GnomAD database, including 20,971 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 0.52 ( 20971 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35

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=-0.57).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 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:

0.524

AC:

79538

AN:

151924

Hom.:

20955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.429

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.531

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

GnomAD4 genome

AF:

0.523

AC:

79585

AN:

152042

Hom.:

20971

Cov.:

AF XY:

0.524

AC XY:

38950

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.475

Gnomad4 ASJ

AF:

0.505

Gnomad4 EAS

AF:

0.366

Gnomad4 SAS

AF:

0.665

Gnomad4 FIN

AF:

0.542

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.551

Hom.:

12396

Bravo

AF:

0.510

Asia WGS

AF:

0.505

AC:

1758

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.44

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