Genetic Variant ENST00000532770.2:n.147-13613C>T (chr11-92946612-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 ENST00000532770.2(ENSG00000254874):n.147-13613C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,930 control chromosomes in the GnomAD database, including 10,550 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 0.37 ( 10550 hom., cov: 32)

Consequence

ENSG00000254874
ENST00000532770.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

10 publications found

Variant links:

Genes affected

ENSG00000254874 (HGNC:):

ENSG00000254874 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000254874	ENST00000532770.2 link	n.147-13613C>T	intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1 link	n.129-13613C>T	intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1 link	n.116-13613C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56094

AN:

151812

Hom.:

10546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.481

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.373

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

GnomAD4 genome

AF:

0.370

AC:

56140

AN:

151930

Hom.:

10550

Cov.:

AF XY:

0.370

AC XY:

27482

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.424

AC:

17558

AN:

41416

American (AMR)

AF:

0.287

AC:

4381

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3472

East Asian (EAS)

AF:

0.444

AC:

2284

AN:

5148

South Asian (SAS)

AF:

0.399

AC:

1917

AN:

4806

European-Finnish (FIN)

AF:

0.399

AC:

4213

AN:

10558

Middle Eastern (MID)

AF:

0.370

AC:

108

AN:

292

European-Non Finnish (NFE)

AF:

0.344

AC:

23355

AN:

67946

Other (OTH)

AF:

0.373

AC:

786

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1816

3632

5448

7264

9080

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.350

Hom.:

1309

Bravo

AF:

0.361

Asia WGS

AF:

0.364

AC:

1265

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.0

(source)

DANN

Benign

0.31

PhyloP100

-1.4

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