dbSNP rs1449866: ENSG00000309389:n.84-10534C>A (chr3-143157791-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000840693.1(ENSG00000309389):n.84-10534C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,116 control chromosomes in the GnomAD database, including 3,768 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 0.20 ( 3768 hom., cov: 33)

Consequence

ENSG00000309389
ENST00000840693.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.654

Publications

4 publications found

Variant links:

Genes affected

ENSG00000309389 (HGNC:):

ENSG00000309389 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=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309389	ENST00000840693.1 link	n.84-10534C>A	intron_variant	Intron 1 of 1
ENSG00000309389	ENST00000840694.1 link	n.65-3640C>A	intron_variant	Intron 1 of 2
ENSG00000309389	ENST00000840695.1 link	n.63-3501C>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30440

AN:

151998

Hom.:

3757

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.191

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

GnomAD4 genome

AF:

0.200

AC:

30487

AN:

152116

Hom.:

3768

Cov.:

AF XY:

0.200

AC XY:

14875

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.344

AC:

14276

AN:

41486

American (AMR)

AF:

0.195

AC:

2971

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.104

AC:

362

AN:

3468

East Asian (EAS)

AF:

0.189

AC:

981

AN:

5184

South Asian (SAS)

AF:

0.270

AC:

1301

AN:

4818

European-Finnish (FIN)

AF:

0.118

AC:

1247

AN:

10588

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8725

AN:

67980

Other (OTH)

AF:

0.193

AC:

408

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1199

2399

3598

4798

5997

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.153

Hom.:

2104

Bravo

AF:

0.214

Asia WGS

AF:

0.255

AC:

888

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

0.65

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