dbSNP rs6476179: ENSG00000310559:n.227+43397T>C (chr9-29985817-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 ENST00000850881.1(ENSG00000310559):n.227+43397T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,924 control chromosomes in the GnomAD database, including 3,415 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 0.19 ( 3415 hom., cov: 32)

Consequence

ENSG00000310559
ENST00000850881.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

2 publications found

Variant links:

Genes affected

ENSG00000310559 (HGNC:):

ENSG00000310559 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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
ENSG00000310559	ENST00000850881.1 link	n.227+43397T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28569

AN:

151806

Hom.:

3410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.0975

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.190

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

GnomAD4 genome

AF:

0.188

AC:

28599

AN:

151924

Hom.:

3415

Cov.:

AF XY:

0.184

AC XY:

13670

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.331

AC:

13706

AN:

41416

American (AMR)

AF:

0.145

AC:

2215

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

522

AN:

3464

East Asian (EAS)

AF:

0.189

AC:

972

AN:

5152

South Asian (SAS)

AF:

0.186

AC:

891

AN:

4802

European-Finnish (FIN)

AF:

0.0975

AC:

1032

AN:

10590

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8715

AN:

67944

Other (OTH)

AF:

0.189

AC:

398

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1087

2175

3262

4350

5437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.151

Hom.:

6777

Bravo

AF:

0.195

Asia WGS

AF:

0.225

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.2

(source)

DANN

Benign

0.53

PhyloP100

-1.3

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