Genetic Variant ENSG00000244337:n.62-3115C>T (chr2-131961907-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000421696.2(ENSG00000244337):n.62-3115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 149,956 control chromosomes in the GnomAD database, including 59,131 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 0.89 ( 59131 hom., cov: 26)

Consequence

ENSG00000244337
ENST00000421696.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.517

Publications

1 publications found

Variant links:

Genes affected

ENSG00000244337 (HGNC:):

ENSG00000244337 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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
ENSG00000244337	ENST00000421696.2 link	n.62-3115C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.887

AC:

132917

AN:

149852

Hom.:

59085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.932

Gnomad AMI

AF:

0.844

Gnomad AMR

AF:

0.884

Gnomad ASJ

AF:

0.852

Gnomad EAS

AF:

0.995

Gnomad SAS

AF:

0.853

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.866

Gnomad OTH

AF:

0.866

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

GnomAD4 genome

AF:

0.887

AC:

133017

AN:

149956

Hom.:

59131

Cov.:

AF XY:

0.884

AC XY:

64793

AN XY:

73254

show subpopulations

African (AFR)

AF:

0.932

AC:

37063

AN:

39774

American (AMR)

AF:

0.884

AC:

13436

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.852

AC:

2954

AN:

3466

East Asian (EAS)

AF:

0.994

AC:

5123

AN:

5152

South Asian (SAS)

AF:

0.853

AC:

4062

AN:

4762

European-Finnish (FIN)

AF:

0.840

AC:

8854

AN:

10538

Middle Eastern (MID)

AF:

0.830

AC:

244

AN:

294

European-Non Finnish (NFE)

AF:

0.866

AC:

58698

AN:

67772

Other (OTH)

AF:

0.867

AC:

1813

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.448

Heterozygous variant carriers

675

1350

2025

2700

3375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<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:

0.888

Hom.:

8107

Bravo

AF:

0.891

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.47

PhyloP100

-0.52

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