rs35474563

Positions:

• chrY-20756109-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2 BP4_Strong BS2

The NM_001039567.3(RPS4Y2):​c.-55C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000817 in 345,309 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 0)
  • Exomes 𝑓: 0.00082 (0 hom. 282 hem.)
• Consequence: RPS4Y2 NM_001039567.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

RPS4Y2 (HGNC:18501): (ribosomal protein S4 Y-linked 2) The protein encoded by this gene is a ribosomal protein that is highly similar to RPS4Y1. This gene is located in the male-specific region of the Y chromosome. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS2: High Hemizygotes in GnomAdExome4 at 282 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS4Y2	NM_001039567.3	c.-55C>T		5_prime_UTR_variant	1/7	ENST00000629237.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS4Y2	ENST00000629237.2	c.-55C>T		5_prime_UTR_variant	1/7	1	NM_001039567.3	P1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.000817 AC: 282 AN: 345309 Hom.: 0 AF XY: 0.000817 AC XY: 282 AN XY: 345309

Gnomad4 AFR exome AF: 0.000591

Gnomad4 AMR exome AF: 0.00230

Gnomad4 ASJ exome AF: 0.000153

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000289

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000846

Gnomad4 OTH exome AF: 0.00190

GnomAD4 genome Cov.: 0

Alfa AF: 0.000764 Hom.: 38

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35474563; hg19: chrY-22917995;