dbSNP rs10491753: ENSG00000226197:n.113-7488A>C (chr9-13545787-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664438.1(ENSG00000226197):n.113-7488A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,290 control chromosomes in the GnomAD database, including 277 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 0.050 ( 277 hom., cov: 32)

Consequence

ENSG00000226197
ENST00000664438.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.304

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0753 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	ENST00000664438.1 link	n.113-7488A>C	intron_variant	Intron 1 of 2
ENSG00000226197	ENST00000840201.1 link	n.289-7488A>C	intron_variant	Intron 2 of 3
ENSG00000226197	ENST00000840202.1 link	n.773-7488A>C	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.0499

AC:

7598

AN:

152172

Hom.:

277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0151

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.0514

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0203

Gnomad FIN

AF:

0.0354

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0771

Gnomad OTH

AF:

0.0584

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

GnomAD4 genome

AF:

0.0498

AC:

7591

AN:

152290

Hom.:

277

Cov.:

AF XY:

0.0466

AC XY:

3466

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0151

AC:

627

AN:

41572

American (AMR)

AF:

0.0513

AC:

784

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0389

AC:

135

AN:

3468

East Asian (EAS)

AF:

0.000579

AC:

AN:

5178

South Asian (SAS)

AF:

0.0201

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0354

AC:

376

AN:

10628

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0770

AC:

5240

AN:

68026

Other (OTH)

AF:

0.0582

AC:

123

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

356

712

1068

1424

1780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0681

Hom.:

204

Bravo

AF:

0.0497

Asia WGS

AF:

0.0140

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.33

(source)

DANN

Benign

0.44

PhyloP100

-0.30

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