NM_001258249.2:c.2964+537G>A

Variant names:

• chrY-13325684-C-T
• rs2032666
• NM_001258249.2:c.2964+537G>A

Variant summary

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

The NM_001258249.2(UTY):​c.2964+537G>A variant causes a intron 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 0.0046 (0 hom., 153 hem., cov: 0)
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTY	NM_001258249.2	c.2964+537G>A		intron_variant	Intron 19 of 29	ENST00000545955.6	NP_001245178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTY	ENST00000545955.6	c.2964+537G>A		intron_variant	Intron 19 of 29	1	NM_001258249.2	ENSP00000442047.2

Frequencies

GnomAD3 genomes AF: 0.00457 AC: 153 AN: 33496 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000348

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000547

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0656

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000520

Gnomad OTH AF: 0.00210

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00456 AC: 153 AN: 33565 Hom.: 0 Cov.: 0 AF XY: 0.00456 AC XY: 153 AN XY: 33565

African (AFR) AF: 0.000345 AC: 3 AN: 8686

American (AMR) AF: 0.000546 AC: 2 AN: 3663

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 777

East Asian (EAS) AF: 0.0664 AC: 85 AN: 1281

South Asian (SAS) AF: 0.0358 AC: 55 AN: 1537

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3385

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

European-Non Finnish (NFE) AF: 0.000520 AC: 7 AN: 13463

Other (OTH) AF: 0.00208 AC: 1 AN: 480

Alfa AF: 0.0352 Hom.: 1122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		-0.55

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: rs2032666; hg19: chrY-15437564;