dbSNP rs9379851: ENSG00000291336:n.1000-198635A>C (chr6-26354552-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 ENST00000707189.1(ENSG00000291336):n.1000-198635A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 152,256 control chromosomes in the GnomAD database, including 567 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 0.077 ( 567 hom., cov: 32)

Consequence

ENSG00000291336
ENST00000707189.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21

Publications

32 publications found

Variant links:

Genes affected

ENSG00000291336 (HGNC:):

ENSG00000291336 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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291336	ENST00000707189.1 link	n.1000-198635A>C	intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1 link	n.1001-178153A>C	intron_variant	Intron 1 of 1
ENSG00000300412	ENST00000771472.1 link	n.160-995A>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0770

AC:

11718

AN:

152138

Hom.:

568

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0344

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.0410

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.0864

Gnomad SAS

AF:

0.0983

Gnomad FIN

AF:

0.0713

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.0701

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

GnomAD4 genome

AF:

0.0769

AC:

11709

AN:

152256

Hom.:

567

Cov.:

AF XY:

0.0737

AC XY:

5489

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0344

AC:

1429

AN:

41550

American (AMR)

AF:

0.0408

AC:

624

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3470

East Asian (EAS)

AF:

0.0866

AC:

448

AN:

5174

South Asian (SAS)

AF:

0.0972

AC:

469

AN:

4826

European-Finnish (FIN)

AF:

0.0713

AC:

757

AN:

10616

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.111

AC:

7543

AN:

68006

Other (OTH)

AF:

0.0703

AC:

148

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

548

1096

1645

2193

2741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.103

Hom.:

1721

Bravo

AF:

0.0721

Asia WGS

AF:

0.0990

AC:

344

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.75

(source)

DANN

Benign

0.40

PhyloP100

-2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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