10-14887472-G-C

Variant names:

• chr10-14887472-G-C
• rs17156024
• NM_001193424.2:c.177+5827G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001193424.2(SUV39H2):​c.177+5827G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,118 control chromosomes in the GnomAD database, including 3,370 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 0.16 (3370 hom., cov: 32)
• Consequence: SUV39H2 NM_001193424.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) 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
SUV39H2	NM_001193424.2	c.177+5827G>C		intron_variant	Intron 2 of 5	ENST00000354919.11	NP_001180353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUV39H2	ENST00000354919.11	c.177+5827G>C		intron_variant	Intron 2 of 5	5	NM_001193424.2	ENSP00000346997.6

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24510 AN: 152000 Hom.: 3348 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.162 AC: 24577 AN: 152118 Hom.: 3370 Cov.: 32 AF XY: 0.163 AC XY: 12142 AN XY: 74362

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0691

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0560

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0990 Hom.: 199

Bravo AF: 0.177

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.36

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

Other links and lift over

dbSNP: rs17156024; hg19: chr10-14929471;