dbSNP rs2294405: :null (chr6-98844260-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.306 in 152,188 control chromosomes in the GnomAD database, including 7,972 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 0.31 ( 7972 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.79

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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:

0.306

AC:

46542

AN:

152070

Hom.:

7962

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.704

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.294

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

GnomAD4 genome

AF:

0.306

AC:

46572

AN:

152188

Hom.:

7972

Cov.:

AF XY:

0.310

AC XY:

23044

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.370

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.703

Gnomad4 SAS

AF:

0.378

Gnomad4 FIN

AF:

0.322

Gnomad4 NFE

AF:

0.318

Gnomad4 OTH

AF:

0.297

Alfa

AF:

0.294

Hom.:

3521

Bravo

AF:

0.307

Asia WGS

AF:

0.497

AC:

1729

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.87

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