dbSNP rs13061797: ENSG00000240354:n.158-5235A>G (chr3-161827209-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000497285.2(ENSG00000240354):n.158-5235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,642 control chromosomes in the GnomAD database, including 1,513 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 0.13 ( 1513 hom., cov: 32)

Consequence

ENSG00000240354
ENST00000497285.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.556

Publications

4 publications found

Variant links:

Genes affected

ENSG00000240354 (HGNC:):

ENSG00000240354 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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
ENSG00000240354	ENST00000497285.2 link	n.158-5235A>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20288

AN:

151524

Hom.:

1512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0117

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0962

Gnomad MID

AF:

0.217

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.145

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

GnomAD4 genome

AF:

0.134

AC:

20296

AN:

151642

Hom.:

1513

Cov.:

AF XY:

0.130

AC XY:

9658

AN XY:

74106

show subpopulations

African (AFR)

AF:

0.154

AC:

6376

AN:

41386

American (AMR)

AF:

0.121

AC:

1847

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

477

AN:

3462

East Asian (EAS)

AF:

0.0115

AC:

AN:

5130

South Asian (SAS)

AF:

0.105

AC:

506

AN:

4820

European-Finnish (FIN)

AF:

0.0962

AC:

1016

AN:

10558

Middle Eastern (MID)

AF:

0.209

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.142

AC:

9612

AN:

67760

Other (OTH)

AF:

0.145

AC:

304

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

794

1588

2382

3176

3970

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.139

Hom.:

3785

Bravo

AF:

0.136

Asia WGS

AF:

0.0710

AC:

249

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.1

(source)

DANN

Benign

0.75

PhyloP100

0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over