Genetic Variant ENSG00000301354:n.109+23146T>C (chr9-75414429-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 ENST00000778465.1(ENSG00000301354):n.109+23146T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,190 control chromosomes in the GnomAD database, including 1,665 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 0.14 ( 1665 hom., cov: 32)

Consequence

ENSG00000301354
ENST00000778465.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.906

Publications

1 publications found

Variant links:

Genes affected

ENSG00000301354 (HGNC:):

ENSG00000301354 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=-0.6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 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
ENSG00000301354	ENST00000778465.1 link	n.109+23146T>C		intron_variant	Intron 1 of 1
ENSG00000301354	ENST00000778466.1 link	n.271+8397T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21429

AN:

152072

Hom.:

1664

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.0824

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.141

AC:

21468

AN:

152190

Hom.:

1665

Cov.:

AF XY:

0.143

AC XY:

10632

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.185

AC:

7662

AN:

41500

American (AMR)

AF:

0.161

AC:

2462

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0824

AC:

286

AN:

3470

East Asian (EAS)

AF:

0.183

AC:

949

AN:

5178

South Asian (SAS)

AF:

0.156

AC:

749

AN:

4810

European-Finnish (FIN)

AF:

0.127

AC:

1345

AN:

10610

Middle Eastern (MID)

AF:

0.0993

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.112

AC:

7596

AN:

68018

Other (OTH)

AF:

0.125

AC:

264

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

930

1861

2791

3722

4652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.122

Hom.:

4394

Bravo

AF:

0.144

Asia WGS

AF:

0.186

AC:

643

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

7.3

(source)

DANN

Benign

0.58

PhyloP100

0.91

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