Genetic Variant ENSG00000295576:n.194+22494T>C (chr13-33722889-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000731018.1(ENSG00000295576):n.194+22494T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 152,236 control chromosomes in the GnomAD database, including 997 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 0.077 ( 997 hom., cov: 32)

Consequence

ENSG00000295576
ENST00000731018.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250

Publications

2 publications found

Variant links:

Genes affected

ENSG00000295576 (HGNC:):

ENSG00000295576 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 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
ENSG00000295576	ENST00000731018.1 link	n.194+22494T>C		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1 link	n.51-38944T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0771

AC:

11734

AN:

152118

Hom.:

993

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0727

Gnomad ASJ

AF:

0.0110

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.0494

Gnomad FIN

AF:

0.0230

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0110

Gnomad OTH

AF:

0.0640

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

GnomAD4 genome

AF:

0.0773

AC:

11772

AN:

152236

Hom.:

997

Cov.:

AF XY:

0.0786

AC XY:

5850

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.191

AC:

7937

AN:

41516

American (AMR)

AF:

0.0730

AC:

1117

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0110

AC:

AN:

3468

East Asian (EAS)

AF:

0.252

AC:

1305

AN:

5184

South Asian (SAS)

AF:

0.0491

AC:

237

AN:

4830

European-Finnish (FIN)

AF:

0.0230

AC:

244

AN:

10612

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0110

AC:

751

AN:

68012

Other (OTH)

AF:

0.0633

AC:

134

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

504

1008

1511

2015

2519

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0417

Hom.:

128

Bravo

AF:

0.0881

Asia WGS

AF:

0.174

AC:

603

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.1

(source)

DANN

Benign

0.70

PhyloP100

0.25

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