dbSNP rs10255295: ENSG00000225559:n.282+10518A>G (chr7-138174020-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000834913.1(ENSG00000225559):n.282+10518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,936 control chromosomes in the GnomAD database, including 910 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 0.10 ( 910 hom., cov: 31)

Consequence

ENSG00000225559
ENST00000834913.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164

Publications

4 publications found

Variant links:

Genes affected

ENSG00000225559 (HGNC:):

ENSG00000225559 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000225559	ENST00000834913.1 link	n.282+10518A>G	intron_variant	Intron 2 of 2
ENSG00000225559	ENST00000834914.1 link	n.263-8811A>G	intron_variant	Intron 2 of 3
ENSG00000225559	ENST00000834915.1 link	n.261-8811A>G	intron_variant	Intron 2 of 3
ENSG00000225559	ENST00000834916.1 link	n.396+1919A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15736

AN:

151818

Hom.:

908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.0955

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.00309

Gnomad SAS

AF:

0.0636

Gnomad FIN

AF:

0.0825

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.106

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

GnomAD4 genome

AF:

0.104

AC:

15752

AN:

151936

Hom.:

910

Cov.:

AF XY:

0.0998

AC XY:

7412

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.101

AC:

4178

AN:

41404

American (AMR)

AF:

0.0953

AC:

1454

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

410

AN:

3470

East Asian (EAS)

AF:

0.00310

AC:

AN:

5162

South Asian (SAS)

AF:

0.0634

AC:

305

AN:

4808

European-Finnish (FIN)

AF:

0.0825

AC:

873

AN:

10578

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8128

AN:

67950

Other (OTH)

AF:

0.105

AC:

222

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

713

1425

2138

2850

3563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.115

Hom.:

1336

Bravo

AF:

0.105

Asia WGS

AF:

0.0440

AC:

156

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.7

(source)

DANN

Benign

0.65

PhyloP100

0.16

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