dbSNP rs4798774: :null (chr18-932568-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 152,010 control chromosomes in the GnomAD database, including 13,674 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 ( 13674 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.393

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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:

59726

AN:

151892

Hom.:

13666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.405

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

GnomAD4 genome

AF:

0.393

AC:

59767

AN:

152010

Hom.:

13674

Cov.:

AF XY:

0.393

AC XY:

29188

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.320

Gnomad4 SAS

AF:

0.316

Gnomad4 FIN

AF:

0.520

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.407

Alfa

AF:

0.480

Hom.:

35420

Bravo

AF:

0.383

Asia WGS

AF:

0.307

AC:

1068

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.9

DANN

Benign

0.56

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