dbSNP rs983037: ENSG00000225649:n.1842-24167T>G (chr2-12940094-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000655303.2(ENSG00000225649):n.1842-24167T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,830 control chromosomes in the GnomAD database, including 6,304 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 0.27 ( 6304 hom., cov: 32)

Consequence

ENSG00000225649
ENST00000655303.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.740

Publications

3 publications found

Variant links:

Genes affected

ENSG00000225649 (HGNC:):

ENSG00000225649 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) 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
ENSG00000225649	ENST00000655303.2 link	n.1842-24167T>G	intron_variant	Intron 3 of 4
ENSG00000225649	ENST00000663507.1 link	n.237-24167T>G	intron_variant	Intron 2 of 6
ENSG00000225649	ENST00000664540.1 link	n.570-24167T>G	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41636

AN:

151712

Hom.:

6301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.445

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.0387

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.357

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.276

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

GnomAD4 genome

AF:

0.274

AC:

41644

AN:

151830

Hom.:

6304

Cov.:

AF XY:

0.270

AC XY:

20043

AN XY:

74184

show subpopulations

African (AFR)

AF:

0.191

AC:

7908

AN:

41492

American (AMR)

AF:

0.221

AC:

3373

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

1260

AN:

3464

East Asian (EAS)

AF:

0.0388

AC:

201

AN:

5180

South Asian (SAS)

AF:

0.176

AC:

849

AN:

4812

European-Finnish (FIN)

AF:

0.357

AC:

3759

AN:

10534

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23218

AN:

67772

Other (OTH)

AF:

0.272

AC:

574

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1468

2936

4405

5873

7341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.318

Hom.:

3991

Bravo

AF:

0.260

Asia WGS

AF:

0.109

AC:

379

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.76

(source)

DANN

Benign

0.82

PhyloP100

-0.74

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