Genetic Variant ENSG00000293611:n.111+14163T>G (chr2-57867738-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 ENST00000715880.1(ENSG00000293611):n.111+14163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,044 control chromosomes in the GnomAD database, including 38,456 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 0.70 ( 38456 hom., cov: 31)

Consequence

ENSG00000293611
ENST00000715880.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.342

Publications

13 publications found

Variant links:

Genes affected

ENSG00000293611 (HGNC:):

ENSG00000293611 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293611	ENST00000715880.1 link	n.111+14163T>G	intron_variant	Intron 1 of 2
ENSG00000293611	ENST00000715881.1 link	n.121+18438T>G	intron_variant	Intron 1 of 2
ENSG00000285755	ENST00000811253.1 link	n.102+18768T>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.698

AC:

106015

AN:

151926

Hom.:

38408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.918

Gnomad AMI

AF:

0.719

Gnomad AMR

AF:

0.609

Gnomad ASJ

AF:

0.642

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.634

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.673

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

GnomAD4 genome

AF:

0.698

AC:

106121

AN:

152044

Hom.:

38456

Cov.:

AF XY:

0.694

AC XY:

51563

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.918

AC:

38095

AN:

41506

American (AMR)

AF:

0.609

AC:

9284

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.642

AC:

2227

AN:

3468

East Asian (EAS)

AF:

0.609

AC:

3146

AN:

5168

South Asian (SAS)

AF:

0.567

AC:

2735

AN:

4820

European-Finnish (FIN)

AF:

0.634

AC:

6708

AN:

10574

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.613

AC:

41653

AN:

67932

Other (OTH)

AF:

0.670

AC:

1418

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1529

3057

4586

6114

7643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<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:

0.649

Hom.:

47482

Bravo

AF:

0.706

Asia WGS

AF:

0.614

AC:

2136

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.3

(source)

DANN

Benign

0.41

PhyloP100

0.34

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