rs16980601

Variant names:

• chrY-13303235-A-G
• rs16980601
• NM_001258249.2:c.3566-244T>C

Your query was ambiguous. Multiple possible variants found:

• chrY-13303235-A-G
• chrY-13303235-A-T

Variant summary

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

The NM_001258249.2(UTY):​c.3566-244T>C 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 0.031 (0 hom., 1042 hem., cov: 0)
• Consequence: UTY NM_001258249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258249.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	NM_001258249.2	MANE Select	c.3566-244T>C		intron	N/A	NP_001245178.1
	UTY	NM_001400170.1		c.3410-244T>C		intron	N/A	NP_001387099.1
	UTY	NM_001400171.1		c.3365-244T>C		intron	N/A	NP_001387100.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	ENST00000545955.6	TSL:1 MANE Select	c.3566-244T>C		intron	N/A	ENSP00000442047.2
	UTY	ENST00000382896.9	TSL:1	c.3500-244T>C		intron	N/A	ENSP00000372352.5
	UTY	ENST00000617789.5	TSL:1	c.3431-244T>C		intron	N/A	ENSP00000483735.1

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 1042 AN: 33615 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00209

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00162

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.0262

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000737

Gnomad OTH AF: 0.0275

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

GnomAD4 genome AF: 0.0309 AC: 1042 AN: 33679 Hom.: 0 Cov.: 0 AF XY: 0.0309 AC XY: 1042 AN XY: 33679

African (AFR) AF: 0.00208 AC: 18 AN: 8649

American (AMR) AF: 0.00162 AC: 6 AN: 3700

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 766

East Asian (EAS) AF: 0.773 AC: 965 AN: 1249

South Asian (SAS) AF: 0.0261 AC: 40 AN: 1531

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3462

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 75

European-Non Finnish (NFE) AF: 0.0000737 AC: 1 AN: 13560

Other (OTH) AF: 0.0253 AC: 12 AN: 475

Alfa AF: 0.0462 Hom.: 1673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.14
PhyloP100		-0.21
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: rs16980601; hg19: chrY-15415115;