dbSNP rs4434089: :null (chr22-23041683-A-G) – 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 0.62 in 152,156 control chromosomes in the GnomAD database, including 32,522 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 0.62 ( 32522 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.173

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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:

0.620

AC:

94319

AN:

152038

Hom.:

32504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.516

Gnomad AMR

AF:

0.751

Gnomad ASJ

AF:

0.730

Gnomad EAS

AF:

0.990

Gnomad SAS

AF:

0.769

Gnomad FIN

AF:

0.799

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.660

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

GnomAD4 genome

AF:

0.620

AC:

94370

AN:

152156

Hom.:

32522

Cov.:

AF XY:

0.630

AC XY:

46900

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.307

Gnomad4 AMR

AF:

0.752

Gnomad4 ASJ

AF:

0.730

Gnomad4 EAS

AF:

0.990

Gnomad4 SAS

AF:

0.770

Gnomad4 FIN

AF:

0.799

Gnomad4 NFE

AF:

0.709

Gnomad4 OTH

AF:

0.664

Alfa

AF:

0.681

Hom.:

12369

Bravo

AF:

0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.1

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