Genetic Variant ENSG00000293833:n.286+17507C>T (chr2-76532449-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 ENST00000719311.1(ENSG00000293833):n.286+17507C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,044 control chromosomes in the GnomAD database, including 370 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 0.066 ( 370 hom., cov: 32)

Consequence

ENSG00000293833
ENST00000719311.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.439

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293833 (HGNC:):

ENSG00000293833 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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0784 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
ENSG00000293833	ENST00000719311.1 link	n.286+17507C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0656

AC:

9972

AN:

151928

Hom.:

369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0587

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0822

Gnomad ASJ

AF:

0.0657

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0322

Gnomad FIN

AF:

0.0626

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.0736

Gnomad OTH

AF:

0.0887

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

GnomAD4 genome

AF:

0.0656

AC:

9978

AN:

152044

Hom.:

370

Cov.:

AF XY:

0.0649

AC XY:

4824

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0588

AC:

2438

AN:

41472

American (AMR)

AF:

0.0822

AC:

1254

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.0657

AC:

228

AN:

3468

East Asian (EAS)

AF:

0.000387

AC:

AN:

5164

South Asian (SAS)

AF:

0.0318

AC:

153

AN:

4814

European-Finnish (FIN)

AF:

0.0626

AC:

662

AN:

10574

Middle Eastern (MID)

AF:

0.140

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0736

AC:

5006

AN:

67982

Other (OTH)

AF:

0.0878

AC:

185

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

474

949

1423

1898

2372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0575

Hom.:

162

Bravo

AF:

0.0663

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.9

(source)

DANN

Benign

0.61

PhyloP100

-0.44

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