Genetic Variant ENSG00000295576:n.194+22792T>C (chr13-33723187-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+22792T>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 152,226 control chromosomes in the GnomAD database, including 992 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 ( 992 hom., cov: 32)

Consequence

ENSG00000295576
ENST00000731018.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0170

Publications

1 publications found

Variant links:

Genes affected

ENSG00000295576 (HGNC:):

ENSG00000295576 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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+22792T>C		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1 link	n.51-38646T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0771

AC:

11729

AN:

152108

Hom.:

988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0727

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.0509

Gnomad FIN

AF:

0.0231

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0110

Gnomad OTH

AF:

0.0641

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

GnomAD4 genome

AF:

0.0773

AC:

11767

AN:

152226

Hom.:

992

Cov.:

AF XY:

0.0786

AC XY:

5854

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.191

AC:

7934

AN:

41506

American (AMR)

AF:

0.0730

AC:

1116

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0109

AC:

AN:

3472

East Asian (EAS)

AF:

0.251

AC:

1297

AN:

5176

South Asian (SAS)

AF:

0.0506

AC:

244

AN:

4826

European-Finnish (FIN)

AF:

0.0231

AC:

245

AN:

10620

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0110

AC:

750

AN:

68010

Other (OTH)

AF:

0.0634

AC:

134

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

503

1006

1509

2012

2515

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:

0.0198

Hom.:

Bravo

AF:

0.0881

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.017

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