chrY-13360045-T-C

Variant names:

• chrY-13360045-T-C
• rs2032674
• NM_001258249.2:c.966-59A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258249.2(UTY):​c.966-59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 324,808 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: 𝑓 0.11 (0 hom., 3630 hem., cov: 0)
  • Exomes 𝑓: 0.059 (0 hom. 17247 hem.)
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 5 publications found

Genes affected

UTY (HGNC:12638): (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked) This gene encodes a protein containing tetratricopeptide repeats which are thought to be involved in protein-protein interactions. The encoded protein is also a minor histocompatibility antigen which may induce graft rejection of male stem cell grafts. A large number of alternatively spliced transcripts have been observed for this gene, but the full length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2	c.966-59A>G		intron_variant	Intron 11 of 29	ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.966-59A>G		intron_variant	Intron 11 of 29	1	NM_001258249.2	ENSP00000442047.2

Frequencies

GnomAD3 genomes AF: 0.113 AC: 3631 AN: 32188 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00227

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00197

Gnomad ASJ AF: 0.00132

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.0272

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0674

GnomAD4 exome AF: 0.0590 AC: 17247 AN: 292558 Hom.: 0 AF XY: 0.0590 AC XY: 17247 AN XY: 292558

African (AFR) AF: 0.00206 AC: 12 AN: 5839

American (AMR) AF: 0.00427 AC: 33 AN: 7733

Ashkenazi Jewish (ASJ) AF: 0.000331 AC: 2 AN: 6043

East Asian (EAS) AF: 0.693 AC: 6055 AN: 8740

South Asian (SAS) AF: 0.0128 AC: 357 AN: 27963

European-Finnish (FIN) AF: 0.672 AC: 7820 AN: 11634

Middle Eastern (MID) AF: 0.00550 AC: 6 AN: 1090

European-Non Finnish (NFE) AF: 0.00995 AC: 2106 AN: 211589

Other (OTH) AF: 0.0718 AC: 856 AN: 11927

GnomAD4 genome AF: 0.113 AC: 3630 AN: 32250 Hom.: 0 Cov.: 0 AF XY: 0.113 AC XY: 3630 AN XY: 32250

African (AFR) AF: 0.00226 AC: 19 AN: 8419

American (AMR) AF: 0.00197 AC: 7 AN: 3555

Ashkenazi Jewish (ASJ) AF: 0.00132 AC: 1 AN: 756

East Asian (EAS) AF: 0.835 AC: 973 AN: 1165

South Asian (SAS) AF: 0.0272 AC: 39 AN: 1436

European-Finnish (FIN) AF: 0.747 AC: 2178 AN: 2916

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.0289 AC: 384 AN: 13269

Other (OTH) AF: 0.0649 AC: 29 AN: 447

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.7
DANN	Benign	0.17
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs2032674; hg19: chrY-15471925; COSMIC: COSV58870382; COSMIC: COSV58870382;