rs3373

chrX-48708904-G-AchrX-48708904-G-CchrX-48708904-G-T

Variant summary

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

The NM_003173.4(SUV39H1):c.*1334G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.62 (16478 hom., 18800 hem., cov: 21)
  • Exomes 𝑓: 0.67 (5 hom. 15 hem.)
  • Failed GnomAD Quality Control
• Consequence: SUV39H1 NM_003173.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

SUV39H1 (HGNC:11479): (SUV39H1 histone lysine methyltransferase) This gene encodes an evolutionarily-conserved protein containing an N-terminal chromodomain and a C-terminal SET domain. The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, which results in transcriptional gene silencing. Loss of function of this gene disrupts heterochromatin formation and may cause chromosome instability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUV39H1	NM_003173.4	c.*1334G>A		3_prime_UTR_variant	6/6	ENST00000376687.4
SUV39H1	NM_001282166.2	c.*1334G>A		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUV39H1	ENST00000376687.4	c.*1334G>A		3_prime_UTR_variant	6/6	1	NM_003173.4	P1
	ENST00000416061.1	n.126-8199C>T		intron_variant, non_coding_transcript_variant		3
SUV39H1	ENST00000337852.10	c.*1334G>A		3_prime_UTR_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.617 AC: 66877 AN: 108402 Hom.: 16486 Cov.: 21 AF XY: 0.610 AC XY: 18772 AN XY: 30796

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.671

GnomAD4 exome AF: 0.674 AC: 29 AN: 43 Hom.: 5 Cov.: 0 AF XY: 0.652 AC XY: 15 AN XY: 23

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.720

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.617 AC: 66885 AN: 108453 Hom.: 16478 Cov.: 21 AF XY: 0.609 AC XY: 18800 AN XY: 30857

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.669

Alfa AF: 0.733 Hom.: 71303

Bravo AF: 0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3373; hg19: chrX-48567295;