dbSNP rs17563605: ENSG00000293110:n.1074-23913A>G (chr6-126843427-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 ENST00000650684.1(ENSG00000293110):n.1074-23913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,058 control chromosomes in the GnomAD database, including 3,072 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 0.18 ( 3072 hom., cov: 32)

Consequence

ENSG00000293110
ENST00000650684.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0930

Publications

10 publications found

Variant links:

Genes affected

ENSG00000293110 (HGNC:):

ENSG00000293110 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293110	ENST00000650684.1 link	n.1074-23913A>G	intron_variant	Intron 8 of 8
ENSG00000293110	ENST00000650727.1 link	n.1044-23913A>G	intron_variant	Intron 8 of 14
ENSG00000293110	ENST00000650823.1 link	n.1129-23913A>G	intron_variant	Intron 9 of 11

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27367

AN:

151940

Hom.:

3062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0712

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.0216

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.180

AC:

27389

AN:

152058

Hom.:

3072

Cov.:

AF XY:

0.175

AC XY:

12978

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0711

AC:

2952

AN:

41536

American (AMR)

AF:

0.182

AC:

2778

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

579

AN:

3464

East Asian (EAS)

AF:

0.0215

AC:

111

AN:

5172

South Asian (SAS)

AF:

0.204

AC:

983

AN:

4826

European-Finnish (FIN)

AF:

0.181

AC:

1915

AN:

10598

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.256

AC:

17398

AN:

67886

Other (OTH)

AF:

0.185

AC:

390

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1104

2209

3313

4418

5522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.236

Hom.:

4813

Bravo

AF:

0.173

Asia WGS

AF:

0.156

AC:

543

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.0

(source)

DANN

Benign

0.60

PhyloP100

0.093

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