dbSNP rs10070190: :null (chr5-26866262-G-A) – 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 0.609 in 151,704 control chromosomes in the GnomAD database, including 28,876 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 0.61 ( 28876 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0480

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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:

0.609

AC:

92272

AN:

151584

Hom.:

28833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.501

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.828

Gnomad SAS

AF:

0.792

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.783

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.647

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

GnomAD4 genome

AF:

0.609

AC:

92377

AN:

151704

Hom.:

28876

Cov.:

AF XY:

0.614

AC XY:

45475

AN XY:

74118

show subpopulations

Gnomad4 AFR

AF:

0.688

Gnomad4 AMR

AF:

0.703

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.829

Gnomad4 SAS

AF:

0.793

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.649

Alfa

AF:

0.578

Hom.:

5017

Bravo

AF:

0.629

Asia WGS

AF:

0.812

AC:

2824

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.1

DANN

Benign

0.50

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