rs3373

Variant names:

• chrX-48708904-G-A
• rs3373
• NM_003173.4:c.*1334G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-48708904-G-A
• chrX-48708904-G-C
• chrX-48708904-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

ENSG00000232828 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SUV39H1	NM_003173.4	c.*1334G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000376687.4	NP_003164.1
SUV39H1	NM_001282166.2	c.*1334G>A		3_prime_UTR_variant	Exon 6 of 6		NP_001269095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUV39H1	ENST00000376687.4	c.*1334G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_003173.4	ENSP00000365877.4

Frequencies

GnomAD3 genomes AF: 0.617 AC: 66877 AN: 108402 Hom.: 16486 Cov.: 21

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

African (AFR) AF: 0.00 AC: 0 AN: 1

American (AMR) AF: 0.00 AC: 0 AN: 1

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.700 AC: 7 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.720 AC: 18 AN: 25

Other (OTH) AF: 0.667 AC: 4 AN: 6

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

African (AFR) AF: 0.308 AC: 9217 AN: 29899

American (AMR) AF: 0.713 AC: 7311 AN: 10261

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2025 AN: 2603

East Asian (EAS) AF: 0.834 AC: 2834 AN: 3397

South Asian (SAS) AF: 0.648 AC: 1553 AN: 2395

European-Finnish (FIN) AF: 0.673 AC: 3724 AN: 5531

Middle Eastern (MID) AF: 0.843 AC: 182 AN: 216

European-Non Finnish (NFE) AF: 0.740 AC: 38490 AN: 52020

Other (OTH) AF: 0.669 AC: 986 AN: 1474

Alfa AF: 0.698 Hom.: 93345

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
PhyloP100		-0.31
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

Other links and lift over

dbSNP: rs3373; hg19: chrX-48567295;