dbSNP rs4878538: :null (chr9-33425387-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 0.393 in 152,058 control chromosomes in the GnomAD database, including 12,053 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 0.39 ( 12053 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.227

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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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:

0.393

AC:

59744

AN:

151940

Hom.:

12038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.636

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.449

Gnomad OTH

AF:

0.392

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

GnomAD4 genome

AF:

0.393

AC:

59799

AN:

152058

Hom.:

12053

Cov.:

AF XY:

0.390

AC XY:

28987

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.313

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.348

Gnomad4 EAS

AF:

0.345

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.449

Gnomad4 OTH

AF:

0.396

Alfa

AF:

0.430

Hom.:

18459

Bravo

AF:

0.385

Asia WGS

AF:

0.345

AC:

1199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.93

DANN

Benign

0.46

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