NM_001039567.3:c.-55C>T

Variant names:

• chrY-20756109-C-T
• rs35474563
• NM_001039567.3:c.-55C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. 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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• 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 rank	MANE	Protein	UniProt
RPS4Y2	NM_001039567.3	c.-55C>T		5_prime_UTR_variant	Exon 1 of 7	ENST00000629237.2	NP_001034656.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS4Y2	ENST00000629237.2	c.-55C>T		5_prime_UTR_variant	Exon 1 of 7	1	NM_001039567.3	ENSP00000486252.1

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

African (AFR) AF: 0.000591 AC: 4 AN: 6764

American (AMR) AF: 0.00230 AC: 21 AN: 9135

Ashkenazi Jewish (ASJ) AF: 0.000153 AC: 1 AN: 6540

East Asian (EAS) AF: 0.00 AC: 0 AN: 9396

South Asian (SAS) AF: 0.000289 AC: 9 AN: 31184

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12816

Middle Eastern (MID) AF: 0.00381 AC: 6 AN: 1574

European-Non Finnish (NFE) AF: 0.000846 AC: 215 AN: 254219

Other (OTH) AF: 0.00190 AC: 26 AN: 13681

GnomAD4 genome Cov.: 0

Alfa AF: 0.0116 Hom.: 793

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
PhyloP100		-0.51
PromoterAI		0.30	Neutral

Splicing

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

Other links and lift over

dbSNP: rs35474563; hg19: chrY-22917995;