dbSNP rs1352598: ENSG00000287881:n.73+27803G>A (chr2-18431842-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000670548.1(ENSG00000287881):n.73+27803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0050 ( 0 hom., cov: 26)

Failed GnomAD Quality Control

Consequence

ENSG00000287881
ENST00000670548.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.565

Publications

0 publications found

Variant links:

Genes affected

ENSG00000287881 (HGNC:):

ENSG00000287881 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373454	XR_001739302.1 link	n.691+27803G>A		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287881	ENST00000670548.1 link	n.73+27803G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00504

AC:

598

AN:

118652

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00276

Gnomad AMI

AF:

0.0119

Gnomad AMR

AF:

0.00493

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.00240

Gnomad SAS

AF:

0.00626

Gnomad FIN

AF:

0.00118

Gnomad MID

AF:

0.00847

Gnomad NFE

AF:

0.00670

Gnomad OTH

AF:

0.00694

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00504

AC:

598

AN:

118722

Hom.:

Cov.:

AF XY:

0.00480

AC XY:

277

AN XY:

57716

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00275

AC:

AN:

34500

American (AMR)

AF:

0.00502

AC:

AN:

10962

Ashkenazi Jewish (ASJ)

AF:

0.0133

AC:

AN:

2408

East Asian (EAS)

AF:

0.00240

AC:

AN:

4162

South Asian (SAS)

AF:

0.00629

AC:

AN:

3500

European-Finnish (FIN)

AF:

0.00118

AC:

AN:

7642

Middle Eastern (MID)

AF:

0.00467

AC:

AN:

214

European-Non Finnish (NFE)

AF:

0.00670

AC:

356

AN:

53140

Other (OTH)

AF:

0.00686

AC:

AN:

1604

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.314

Heterozygous variant carriers

107

142

178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00233

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.4

(source)

DANN

Benign

0.40

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