Genetic Variant ENSG00000257526:n.554+5793T>C (chr12-76638849-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 ENST00000832799.1(ENSG00000257526):n.554+5793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,230 control chromosomes in the GnomAD database, including 2,556 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 0.15 ( 2556 hom., cov: 32)

Consequence

ENSG00000257526
ENST00000832799.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

7 publications found

Variant links:

Genes affected

ENSG00000257526 (HGNC:):

ENSG00000257526 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369851	XR_945115.3 link	n.172-2200A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257526	ENST00000832799.1 link	n.554+5793T>C		intron_variant	Intron 3 of 5
ENSG00000257526	ENST00000832800.1 link	n.564+5793T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23521

AN:

152112

Hom.:

2545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.636

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.145

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

GnomAD4 genome

AF:

0.155

AC:

23566

AN:

152230

Hom.:

2556

Cov.:

AF XY:

0.162

AC XY:

12033

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.146

AC:

6060

AN:

41550

American (AMR)

AF:

0.129

AC:

1976

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

496

AN:

3470

East Asian (EAS)

AF:

0.636

AC:

3291

AN:

5178

South Asian (SAS)

AF:

0.222

AC:

1072

AN:

4824

European-Finnish (FIN)

AF:

0.197

AC:

2083

AN:

10588

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8179

AN:

68010

Other (OTH)

AF:

0.154

AC:

325

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

950

1900

2851

3801

4751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

264

528

792

1056

1320

<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:

0.124

Hom.:

2149

Bravo

AF:

0.149

Asia WGS

AF:

0.391

AC:

1355

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.87

(source)

DANN

Benign

0.31

PhyloP100

-1.8

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