Genetic Variant ENSG00000295509:n.252-16619G>A (chr9-32625624-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 ENST00000730514.1(ENSG00000295509):n.252-16619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 152,090 control chromosomes in the GnomAD database, including 656 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 0.088 ( 656 hom., cov: 32)

Consequence

ENSG00000295509
ENST00000730514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.267

Variant links:

Genes affected

ENSG00000295509 (HGNC:):

ENSG00000295509 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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 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
ENSG00000295509	ENST00000730514.1 link	n.252-16619G>A		intron_variant	Intron 2 of 3
ENSG00000295509	ENST00000730515.1 link	n.319-16619G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0884

AC:

13441

AN:

151972

Hom.:

659

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0695

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0608

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.0874

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.0990

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0773

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

GnomAD4 genome

AF:

0.0884

AC:

13443

AN:

152090

Hom.:

656

Cov.:

AF XY:

0.0884

AC XY:

6575

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.0695

AC:

2886

AN:

41506

American (AMR)

AF:

0.0607

AC:

928

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0963

AC:

334

AN:

3470

East Asian (EAS)

AF:

0.0870

AC:

449

AN:

5160

South Asian (SAS)

AF:

0.137

AC:

660

AN:

4812

European-Finnish (FIN)

AF:

0.0990

AC:

1047

AN:

10580

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6910

AN:

67972

Other (OTH)

AF:

0.0788

AC:

166

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

607

1213

1820

2426

3033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0938

Hom.:

1188

Bravo

AF:

0.0824

Asia WGS

AF:

0.132

AC:

459

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.1

(source)

DANN

Benign

0.33

PhyloP100

-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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9-32625624-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

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