Genetic Variant ENSG00000254135:n.718-23241T>A (chr5-158565215-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000642039.2(ENSG00000254135):n.718-23241T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,056 control chromosomes in the GnomAD database, including 4,823 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 0.24 ( 4823 hom., cov: 32)

Consequence

ENSG00000254135
ENST00000642039.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.857

Publications

5 publications found

Variant links:

Genes affected

ENSG00000254135 (HGNC:):

ENSG00000254135 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=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 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
ENSG00000254135	ENST00000642039.2 link	n.718-23241T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

37033

AN:

151936

Hom.:

4816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.244

AC:

37068

AN:

152056

Hom.:

4823

Cov.:

AF XY:

0.243

AC XY:

18072

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.295

AC:

12233

AN:

41468

American (AMR)

AF:

0.285

AC:

4361

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.178

AC:

619

AN:

3468

East Asian (EAS)

AF:

0.284

AC:

1469

AN:

5168

South Asian (SAS)

AF:

0.370

AC:

1782

AN:

4812

European-Finnish (FIN)

AF:

0.131

AC:

1388

AN:

10588

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.213

AC:

14479

AN:

67942

Other (OTH)

AF:

0.241

AC:

509

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1414

2828

4243

5657

7071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.123

Hom.:

195

Bravo

AF:

0.255

Asia WGS

AF:

0.333

AC:

1161

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.2

(source)

DANN

Benign

0.76

PhyloP100

0.86

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