Variant rs6902875 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 0.436 in 152,056 control chromosomes in the GnomAD database, including 18,987 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 0.44 ( 18987 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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:

0.436

AC:

66184

AN:

151938

Hom.:

18934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.819

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.344

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.386

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

AC XY:

AN XY:

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.436

AC:

66286

AN:

152056

Hom.:

18987

Cov.:

AF XY:

0.429

AC XY:

31892

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.819

Gnomad4 AMR

AF:

0.290

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.299

Gnomad4 SAS

AF:

0.342

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.289

Gnomad4 OTH

AF:

0.391

Alfa

AF:

0.308

Hom.:

10641

Bravo

AF:

0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.8

DANN

Benign

0.58

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