dbSNP rs2345595: ENSG00000266602:n.326-6394A>C (chr18-1818384-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000653094.1(ENSG00000266602):n.326-6394A>C variant causes a intron change. 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 0.075 ( 252 hom., cov: 13)

Consequence

ENSG00000266602
ENST00000653094.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Variant links:

Genes affected

ENSG00000266602 (HGNC:):

ENSG00000266602 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000266602	ENST00000653094.1 link	n.326-6394A>C	intron_variant	Intron 3 of 5
ENSG00000266602	ENST00000653330.1 link	n.252-6394A>C	intron_variant	Intron 2 of 4
ENSG00000266602	ENST00000655815.1 link	n.252-6394A>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0753

AC:

5886

AN:

78206

Hom.:

251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0924

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0967

Gnomad ASJ

AF:

0.0577

Gnomad EAS

AF:

0.000777

Gnomad SAS

AF:

0.0331

Gnomad FIN

AF:

0.0542

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0720

Gnomad OTH

AF:

0.0800

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

GnomAD4 genome

AF:

0.0752

AC:

5884

AN:

78226

Hom.:

252

Cov.:

AF XY:

0.0746

AC XY:

2677

AN XY:

35866

show subpopulations

Gnomad4 AFR

AF:

0.0923

Gnomad4 AMR

AF:

0.0968

Gnomad4 ASJ

AF:

0.0577

Gnomad4 EAS

AF:

0.000779

Gnomad4 SAS

AF:

0.0329

Gnomad4 FIN

AF:

0.0542

Gnomad4 NFE

AF:

0.0720

Gnomad4 OTH

AF:

0.0789

Alfa

AF:

0.0177

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

4.9

DANN

Benign

0.32

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