dbSNP rs17597976: ENSG00000299339:n.404+26163G>A (chr2-112797059-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 ENST00000762706.1(ENSG00000299339):n.404+26163G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,214 control chromosomes in the GnomAD database, including 780 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 0.094 ( 780 hom., cov: 32)

Consequence

ENSG00000299339
ENST00000762706.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.278

Publications

5 publications found

Variant links:

Genes affected

ENSG00000299339 (HGNC:):

ENSG00000299339 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 = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299339	ENST00000762706.1 link	n.404+26163G>A	intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1 link	n.499+26163G>A	intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1 link	n.265+26163G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0945

AC:

14376

AN:

152096

Hom.:

779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0609

Gnomad AMI

AF:

0.0593

Gnomad AMR

AF:

0.0813

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0860

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.110

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

GnomAD4 genome

AF:

0.0945

AC:

14382

AN:

152214

Hom.:

780

Cov.:

AF XY:

0.0934

AC XY:

6950

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0609

AC:

2529

AN:

41530

American (AMR)

AF:

0.0811

AC:

1241

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

387

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5188

South Asian (SAS)

AF:

0.157

AC:

756

AN:

4824

European-Finnish (FIN)

AF:

0.0860

AC:

910

AN:

10580

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8224

AN:

68008

Other (OTH)

AF:

0.109

AC:

231

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

637

1275

1912

2550

3187

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.0446

Hom.:

Bravo

AF:

0.0908

Asia WGS

AF:

0.0780

AC:

270

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

0.49

(source)

DANN

Benign

0.61

PhyloP100

-0.28

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