dbSNP rs9271640: :null (chr6-32624423-T-C) – ACMG Classification: Benign (-12 pts)

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 0.762 in 151,652 control chromosomes in the GnomAD database, including 44,449 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 0.76 ( 44449 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.762

AC:

115509

AN:

151536

Hom.:

44422

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.808

Gnomad ASJ

AF:

0.908

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.715

Gnomad FIN

AF:

0.745

Gnomad MID

AF:

0.858

Gnomad NFE

AF:

0.809

Gnomad OTH

AF:

0.807

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

GnomAD4 genome

AF:

0.762

AC:

115594

AN:

151652

Hom.:

44449

Cov.:

AF XY:

0.758

AC XY:

56160

AN XY:

74086

show subpopulations

Gnomad4 AFR

AF:

0.668

Gnomad4 AMR

AF:

0.808

Gnomad4 ASJ

AF:

0.908

Gnomad4 EAS

AF:

0.711

Gnomad4 SAS

AF:

0.716

Gnomad4 FIN

AF:

0.745

Gnomad4 NFE

AF:

0.809

Gnomad4 OTH

AF:

0.803

Alfa

AF:

0.781

Hom.:

13362

Bravo

AF:

0.765

Asia WGS

AF:

0.649

AC:

2262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

8.9

DANN

Benign

0.61

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