dbSNP rs10498306: ENSG00000286040:n.127+24337A>G (chr14-29475997-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 ENST00000652296.1(ENSG00000286040):n.127+24337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,094 control chromosomes in the GnomAD database, including 1,504 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 ( 1504 hom., cov: 32)

Consequence

ENSG00000286040
ENST00000652296.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286040 (HGNC:):

ENSG00000286040 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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
ENSG00000286040	ENST00000652296.1 link	n.127+24337A>G		intron_variant	Intron 1 of 4
ENSG00000286040	ENST00000828160.1 link	n.155+24337A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19714

AN:

151976

Hom.:

1499

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.130

AC:

19746

AN:

152094

Hom.:

1504

Cov.:

AF XY:

0.131

AC XY:

9722

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.105

AC:

4363

AN:

41528

American (AMR)

AF:

0.147

AC:

2245

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

604

AN:

3462

East Asian (EAS)

AF:

0.191

AC:

985

AN:

5160

South Asian (SAS)

AF:

0.135

AC:

652

AN:

4826

European-Finnish (FIN)

AF:

0.183

AC:

1940

AN:

10608

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8512

AN:

67948

Other (OTH)

AF:

0.137

AC:

288

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

858

1716

2574

3432

4290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.128

Hom.:

2354

Bravo

AF:

0.126

Asia WGS

AF:

0.165

AC:

574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.6

(source)

DANN

Benign

0.72

PhyloP100

-0.0070

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