Genetic Variant ENST00000731018.1:n.194+22758G>C (chr13-33723153-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 ENST00000731018.1(ENSG00000295576):n.194+22758G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,172 control chromosomes in the GnomAD database, including 999 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 0.078 ( 999 hom., cov: 32)

Consequence

ENSG00000295576
ENST00000731018.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.874

Publications

1 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=-0.92).

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+22758G>C		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1 link	n.51-38680G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0773

AC:

11758

AN:

152054

Hom.:

995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0730

Gnomad ASJ

AF:

0.0110

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.0512

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:

0.0775

AC:

11796

AN:

152172

Hom.:

999

Cov.:

AF XY:

0.0788

AC XY:

5863

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.192

AC:

7955

AN:

41484

American (AMR)

AF:

0.0733

AC:

1120

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0110

AC:

AN:

3470

East Asian (EAS)

AF:

0.251

AC:

1300

AN:

5174

South Asian (SAS)

AF:

0.0508

AC:

245

AN:

4824

European-Finnish (FIN)

AF:

0.0231

AC:

245

AN:

10606

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0110

AC:

750

AN:

68008

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

477

954

1432

1909

2386

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:

0.0457

Hom.:

Bravo

AF:

0.0883

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

-0.92

CADD

Benign

0.22

(source)

DANN

Benign

0.54

PhyloP100

-0.87

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