dbSNP rs9347819: ENSG00000288696:n.311+69714C>T (chr6-164128680-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000850151.1(ENSG00000288696):n.311+69714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0728 in 152,158 control chromosomes in the GnomAD database, including 533 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 0.073 ( 533 hom., cov: 33)

Consequence

ENSG00000288696
ENST00000850151.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.182

Publications

3 publications found

Variant links:

Genes affected

ENSG00000288696 (HGNC:):

ENSG00000288696 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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
ENSG00000288696	ENST00000850151.1 link	n.311+69714C>T		intron_variant	Intron 3 of 4
ENSG00000288696	ENST00000850152.1 link	n.371+69714C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0727

AC:

11050

AN:

152040

Hom.:

529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0806

Gnomad ASJ

AF:

0.0721

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0478

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0410

Gnomad OTH

AF:

0.0674

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

GnomAD4 genome

AF:

0.0728

AC:

11083

AN:

152158

Hom.:

533

Cov.:

AF XY:

0.0757

AC XY:

5635

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.115

AC:

4767

AN:

41494

American (AMR)

AF:

0.0811

AC:

1239

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0721

AC:

250

AN:

3466

East Asian (EAS)

AF:

0.142

AC:

734

AN:

5170

South Asian (SAS)

AF:

0.131

AC:

631

AN:

4814

European-Finnish (FIN)

AF:

0.0478

AC:

506

AN:

10592

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0410

AC:

2789

AN:

68020

Other (OTH)

AF:

0.0662

AC:

140

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

505

1010

1514

2019

2524

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0526

Hom.:

1163

Bravo

AF:

0.0742

Asia WGS

AF:

0.144

AC:

501

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.3

(source)

DANN

Benign

0.80

PhyloP100

-0.18

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