dbSNP rs17190837: ENSG00000226197:n.100+15321A>G (chr9-13401549-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 ENST00000664575.2(ENSG00000226197):n.100+15321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,222 control chromosomes in the GnomAD database, including 995 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 0.11 ( 995 hom., cov: 32)

Consequence

ENSG00000226197
ENST00000664575.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.387

Publications

1 publications found

Variant links:

Genes affected

ENSG00000226197 (HGNC:):

ENSG00000226197 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000226197	ENST00000664575.2 link	n.100+15321A>G	intron_variant	Intron 1 of 3
ENSG00000226197	ENST00000840204.1 link	n.278+22378A>G	intron_variant	Intron 2 of 4
ENSG00000226197	ENST00000840206.1 link	n.96+15321A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15991

AN:

152104

Hom.:

995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0521

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.0166

Gnomad SAS

AF:

0.0478

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.105

AC:

16001

AN:

152222

Hom.:

995

Cov.:

AF XY:

0.102

AC XY:

7619

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0520

AC:

2160

AN:

41564

American (AMR)

AF:

0.103

AC:

1578

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

526

AN:

3470

East Asian (EAS)

AF:

0.0166

AC:

AN:

5176

South Asian (SAS)

AF:

0.0493

AC:

238

AN:

4830

European-Finnish (FIN)

AF:

0.121

AC:

1277

AN:

10594

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9594

AN:

68006

Other (OTH)

AF:

0.120

AC:

254

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

739

1478

2217

2956

3695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.109

Hom.:

143

Bravo

AF:

0.104

Asia WGS

AF:

0.0450

AC:

158

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.2

(source)

DANN

Benign

0.56

PhyloP100

0.39

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