Genetic Variant ENSG00000295542:n.65-6226T>G (chr15-48102389-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000730753.1(ENSG00000295542):n.65-6226T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,138 control chromosomes in the GnomAD database, including 11,564 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 0.25 ( 11564 hom., cov: 33)

Consequence

ENSG00000295542
ENST00000730753.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

1 publications found

Variant links:

Genes affected

ENSG00000295542 (HGNC:):

ENSG00000295542 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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
ENSG00000295542	ENST00000730753.1 link	n.65-6226T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37175

AN:

152020

Hom.:

11525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.640

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.904

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.0142

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00867

Gnomad OTH

AF:

0.193

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

GnomAD4 genome

AF:

0.245

AC:

37275

AN:

152138

Hom.:

11564

Cov.:

AF XY:

0.246

AC XY:

18302

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.641

AC:

26545

AN:

41442

American (AMR)

AF:

0.249

AC:

3811

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

3470

East Asian (EAS)

AF:

0.903

AC:

4662

AN:

5162

South Asian (SAS)

AF:

0.211

AC:

1019

AN:

4820

European-Finnish (FIN)

AF:

0.0142

AC:

151

AN:

10614

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00867

AC:

590

AN:

68016

Other (OTH)

AF:

0.203

AC:

429

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

712

1424

2136

2848

3560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.0477

Hom.:

1051

Bravo

AF:

0.286

Asia WGS

AF:

0.622

AC:

2158

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.26

(source)

DANN

Benign

0.64

PhyloP100

-1.1

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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