Variant rs17353856 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001193424.2(SUV39H2):c.966C>T(p.Tyr322=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,613,652 control chromosomes in the GnomAD database, including 13,659 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 0.095 ( 882 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12777 hom. )

Consequence

SUV39H2
NM_001193424.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.128

Variant links:

Genes affected

SUV39H2 (HGNC:17287): (SUV39H2 histone lysine methyltransferase) Enables S-adenosyl-L-methionine binding activity; histone methyltransferase activity (H3-K9 specific); and zinc ion binding activity. Involved in chromatin assembly or disassembly and chromatin remodeling. Acts upstream of or within cellular response to hypoxia and negative regulation of transcription by RNA polymerase II. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]

SUV39H2 links:

DCLRE1C (HGNC:17642): (DNA cross-link repair 1C) This gene encodes a nuclear protein that is involved in V(D)J recombination and DNA repair. The encoded protein has single-strand-specific 5'-3' exonuclease activity; it also exhibits endonuclease activity on 5' and 3' overhangs and hairpins. The protein also functions in the regulation of the cell cycle in response to DNA damage. Mutations in this gene can cause Athabascan-type severe combined immunodeficiency (SCIDA) and Omenn syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

DCLRE1C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP7

Synonymous conserved (PhyloP=0.128 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUV39H2	NM_001193424.2 linkuse as main transcript	c.966C>T	p.Tyr322=	synonymous_variant	4/6	ENST00000354919.11	NP_001180353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUV39H2	ENST00000354919.11 linkuse as main transcript	c.966C>T	p.Tyr322=	synonymous_variant	4/6	5	NM_001193424.2	ENSP00000346997	P1	Q9H5I1-1

Frequencies

GnomAD3 genomes

AF:

0.0954

AC:

14515

AN:

152096

Hom.:

882

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0311

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.00288

Gnomad SAS

AF:

0.0813

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.0957

GnomAD3 exomes

AF:

0.105

AC:

26228

AN:

250970

Hom.:

1626

AF XY:

0.105

AC XY:

14255

AN XY:

135642

show subpopulations

Gnomad AFR exome

AF:

0.0291

Gnomad AMR exome

AF:

0.114

Gnomad ASJ exome

AF:

0.0708

Gnomad EAS exome

AF:

0.00245

Gnomad SAS exome

AF:

0.0859

Gnomad FIN exome

AF:

0.126

Gnomad NFE exome

AF:

0.133

Gnomad OTH exome

AF:

0.0996

GnomAD4 exome

AF:

0.128

AC:

186402

AN:

1461438

Hom.:

12777

Cov.:

AF XY:

0.126

AC XY:

91663

AN XY:

727000

show subpopulations

Gnomad4 AFR exome

AF:

0.0274

Gnomad4 AMR exome

AF:

0.114

Gnomad4 ASJ exome

AF:

0.0673

Gnomad4 EAS exome

AF:

0.00224

Gnomad4 SAS exome

AF:

0.0882

Gnomad4 FIN exome

AF:

0.125

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.115

GnomAD4 genome

AF:

0.0953

AC:

14512

AN:

152214

Hom.:

882

Cov.:

AF XY:

0.0957

AC XY:

7124

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0310

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.00289

Gnomad4 SAS

AF:

0.0809

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.0961

Alfa

AF:

0.117

Hom.:

746

Bravo

AF:

0.0899

Asia WGS

AF:

0.0430

AC:

149

AN:

3478

EpiCase

AF:

0.129

EpiControl

AF:

0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

5.7

DANN

Benign

0.89

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over