dbSNP rs952148: ENSG00000309971:n.115+692C>T (chr8-20234008-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000846276.1(ENSG00000309971):n.115+692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,264 control chromosomes in the GnomAD database, including 1,055 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 0.11 ( 1055 hom., cov: 32)

Consequence

ENSG00000309971
ENST00000846276.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.935

Publications

2 publications found

Variant links:

Genes affected

ENSG00000309971 (HGNC:):

ENSG00000309971 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=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.169 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
ENSG00000309971	ENST00000846276.1 link	n.115+692C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16850

AN:

152146

Hom.:

1055

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0788

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.0556

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.0847

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.111

AC:

16846

AN:

152264

Hom.:

1055

Cov.:

AF XY:

0.111

AC XY:

8259

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0787

AC:

3269

AN:

41554

American (AMR)

AF:

0.174

AC:

2668

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0556

AC:

193

AN:

3470

East Asian (EAS)

AF:

0.122

AC:

630

AN:

5180

South Asian (SAS)

AF:

0.149

AC:

719

AN:

4824

European-Finnish (FIN)

AF:

0.0847

AC:

898

AN:

10608

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8164

AN:

68010

Other (OTH)

AF:

0.108

AC:

228

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

735

1469

2204

2938

3673

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.114

Hom.:

1993

Bravo

AF:

0.113

Asia WGS

AF:

0.137

AC:

478

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.92

(source)

DANN

Benign

0.75

PhyloP100

-0.94

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