dbSNP rs1259489: ENSG00000286735:n.169+27399C>A (chr3-120526978-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000732215.1(ENSG00000286735):n.169+27399C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,084 control chromosomes in the GnomAD database, including 4,452 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 0.24 ( 4452 hom., cov: 32)

Consequence

ENSG00000286735
ENST00000732215.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0220

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286735 (HGNC:):

ENSG00000286735 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286735	ENST00000732215.1 link	n.169+27399C>A	intron_variant	Intron 2 of 3
ENSG00000286735	ENST00000732216.1 link	n.247-20207C>A	intron_variant	Intron 2 of 2
ENSG00000295741	ENST00000732308.1 link	n.127+33828G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36234

AN:

151966

Hom.:

4443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.0507

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.261

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

GnomAD4 genome

AF:

0.239

AC:

36278

AN:

152084

Hom.:

4452

Cov.:

AF XY:

0.235

AC XY:

17460

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.241

AC:

10001

AN:

41482

American (AMR)

AF:

0.196

AC:

3003

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1233

AN:

3468

East Asian (EAS)

AF:

0.0510

AC:

264

AN:

5172

South Asian (SAS)

AF:

0.234

AC:

1128

AN:

4822

European-Finnish (FIN)

AF:

0.198

AC:

2092

AN:

10564

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.261

AC:

17710

AN:

67968

Other (OTH)

AF:

0.261

AC:

551

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1394

2788

4181

5575

6969

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.188

Hom.:

583

Bravo

AF:

0.237

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.7

(source)

DANN

Benign

0.32

PhyloP100

-0.022

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