dbSNP rs8084125: ENSG00000309801:n.162+10046A>G (chr18-77240802-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 ENST00000844037.1(ENSG00000309801):n.162+10046A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,246 control chromosomes in the GnomAD database, including 1,567 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 0.14 ( 1567 hom., cov: 32)

Consequence

ENSG00000309801
ENST00000844037.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.662

Publications

7 publications found

Variant links:

Genes affected

ENSG00000309801 (HGNC:):

ENSG00000309801 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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 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
ENSG00000309801	ENST00000844037.1 link	n.162+10046A>G		intron_variant	Intron 1 of 1
ENSG00000309801	ENST00000844038.1 link	n.118+9999A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20715

AN:

152128

Hom.:

1570

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0925

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.136

AC:

20714

AN:

152246

Hom.:

1567

Cov.:

AF XY:

0.137

AC XY:

10191

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0926

AC:

3846

AN:

41550

American (AMR)

AF:

0.118

AC:

1803

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

579

AN:

3472

East Asian (EAS)

AF:

0.00154

AC:

AN:

5182

South Asian (SAS)

AF:

0.176

AC:

851

AN:

4832

European-Finnish (FIN)

AF:

0.193

AC:

2041

AN:

10576

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11153

AN:

68012

Other (OTH)

AF:

0.135

AC:

285

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

911

1823

2734

3646

4557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.152

Hom.:

3475

Bravo

AF:

0.128

Asia WGS

AF:

0.0750

AC:

262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

7.5

(source)

DANN

Benign

0.41

PhyloP100

-0.66

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