Variant 9-128691841-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003011.4(SET):c.132-17C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 1,600,674 control chromosomes in the GnomAD database, including 756,334 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.87 ( 60365 hom., cov: 33)

Exomes 𝑓: 0.98 ( 695969 hom. )

Consequence

SET
NM_003011.4 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.361

Variant links:

Genes affected

SET (HGNC:10760): (SET nuclear proto-oncogene) The protein encoded by this gene inhibits acetylation of nucleosomes, especially histone H4, by histone acetylases (HAT). This inhibition is most likely accomplished by masking histone lysines from being acetylated, and the consequence is to silence HAT-dependent transcription. The encoded protein is part of a complex localized to the endoplasmic reticulum but is found in the nucleus and inhibits apoptosis following attack by cytotoxic T lymphocytes. This protein can also enhance DNA replication of the adenovirus genome. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

SET links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 9-128691841-C-T is Benign according to our data. Variant chr9-128691841-C-T is described in ClinVar as [Benign]. Clinvar id is 1332943.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SET	NM_003011.4 linkuse as main transcript	c.132-17C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000322030.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SET	ENST00000322030.13 linkuse as main transcript	c.132-17C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_003011.4	P1	Q01105-2

Frequencies

GnomAD3 genomes

AF:

0.874

AC:

132877

AN:

152110

Hom.:

60342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.952

Gnomad ASJ

AF:

0.981

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.939

Gnomad FIN

AF:

0.970

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.996

Gnomad OTH

AF:

0.904

GnomAD3 exomes

AF:

0.950

AC:

225226

AN:

236980

Hom.:

108203

AF XY:

0.957

AC XY:

123517

AN XY:

129084

show subpopulations

Gnomad AFR exome

AF:

0.581

Gnomad AMR exome

AF:

0.968

Gnomad ASJ exome

AF:

0.980

Gnomad EAS exome

AF:

0.906

Gnomad SAS exome

AF:

0.949

Gnomad FIN exome

AF:

0.974

Gnomad NFE exome

AF:

0.995

Gnomad OTH exome

AF:

0.968

GnomAD4 exome

AF:

0.978

AC:

1416538

AN:

1448446

Hom.:

695969

Cov.:

AF XY:

0.979

AC XY:

704631

AN XY:

720022

show subpopulations

Gnomad4 AFR exome

AF:

0.573

Gnomad4 AMR exome

AF:

0.966

Gnomad4 ASJ exome

AF:

0.982

Gnomad4 EAS exome

AF:

0.884

Gnomad4 SAS exome

AF:

0.951

Gnomad4 FIN exome

AF:

0.975

Gnomad4 NFE exome

AF:

0.997

Gnomad4 OTH exome

AF:

0.959

GnomAD4 genome

AF:

0.873

AC:

132938

AN:

152228

Hom.:

60365

Cov.:

AF XY:

0.873

AC XY:

65024

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.592

Gnomad4 AMR

AF:

0.952

Gnomad4 ASJ

AF:

0.981

Gnomad4 EAS

AF:

0.901

Gnomad4 SAS

AF:

0.939

Gnomad4 FIN

AF:

0.970

Gnomad4 NFE

AF:

0.996

Gnomad4 OTH

AF:

0.903

Alfa

AF:

0.947

Hom.:

12726

Bravo

AF:

0.858

Asia WGS

AF:

0.895

AC:

3113

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Intellectual disability, autosomal dominant 58

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.38

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over