Genetic Variant ENST00000762706.1:n.404+25195A>G (chr2-112796091-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000762706.1(ENSG00000299339):n.404+25195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,058 control chromosomes in the GnomAD database, including 8,041 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 0.31 ( 8041 hom., cov: 31)

Consequence

ENSG00000299339
ENST00000762706.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510

Publications

15 publications found

Variant links:

COSMIC-nc: COSV60092694

Genes affected

ENSG00000299339 (HGNC:):

ENSG00000299339 links:

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new If you want to explore the variant's impact on the transcript ENST00000762706.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000299339	ENST00000762706.1	n.404+25195A>G	intron	N/A
ENSG00000299339	ENST00000762707.1	n.499+25195A>G	intron	N/A
ENSG00000299339	ENST00000762708.1	n.265+25195A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46966

AN:

151940

Hom.:

8025

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.708

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.402

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.315

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

GnomAD4 genome

AF:

0.309

AC:

47001

AN:

152058

Hom.:

8041

Cov.:

AF XY:

0.318

AC XY:

23621

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.220

AC:

9108

AN:

41472

American (AMR)

AF:

0.398

AC:

6082

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

929

AN:

3470

East Asian (EAS)

AF:

0.709

AC:

3667

AN:

5174

South Asian (SAS)

AF:

0.314

AC:

1516

AN:

4826

European-Finnish (FIN)

AF:

0.402

AC:

4238

AN:

10540

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20513

AN:

67980

Other (OTH)

AF:

0.319

AC:

674

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1593

3186

4779

6372

7965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.307

Hom.:

33535

Bravo

AF:

0.311

Asia WGS

AF:

0.482

AC:

1671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.3

(source)

DANN

Benign

0.36

PhyloP100

-0.051

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over