Genetic Variant ENSG00000293937:n.90+13302C>G (chr2-105722179-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000720028.1(ENSG00000293937):n.90+13302C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,974 control chromosomes in the GnomAD database, including 10,665 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 0.36 ( 10665 hom., cov: 32)

Consequence

ENSG00000293937
ENST00000720028.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Publications

2 publications found

Variant links:

Genes affected

ENSG00000293937 (HGNC:):

ENSG00000293937 links:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293937	ENST00000720028.1 link	n.90+13302C>G		intron_variant	Intron 1 of 1
ENSG00000293937	ENST00000720029.1 link	n.259+11981C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55395

AN:

151856

Hom.:

10649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.314

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.403

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.342

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

GnomAD4 genome

AF:

0.365

AC:

55456

AN:

151974

Hom.:

10665

Cov.:

AF XY:

0.366

AC XY:

27213

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.492

AC:

20381

AN:

41450

American (AMR)

AF:

0.359

AC:

5489

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

902

AN:

3468

East Asian (EAS)

AF:

0.403

AC:

2075

AN:

5150

South Asian (SAS)

AF:

0.314

AC:

1513

AN:

4812

European-Finnish (FIN)

AF:

0.359

AC:

3788

AN:

10560

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20224

AN:

67940

Other (OTH)

AF:

0.342

AC:

721

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1795

3589

5384

7178

8973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

528

1056

1584

2112

2640

<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:

0.175

Hom.:

352

Bravo

AF:

0.371

Asia WGS

AF:

0.359

AC:

1248

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.7

(source)

DANN

Benign

0.64

PhyloP100

-0.17

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