NM_001258249.2:c.3197G>A

Variant names:

• chrY-13323634-C-T
• rs547367934
• NM_001258249.2:c.3197G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Moderate BP6_Moderate BS2

The NM_001258249.2(UTY):​c.3197G>A​(p.Arg1066His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00021 (0 hom., 7 hem., cov: 0)
  • Exomes 𝑓: 0.00021 (0 hom. 75 hem.)
  • Failed GnomAD Quality Control
• Consequence: UTY NM_001258249.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.41
• Publications: 0 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.1578125).
• BP6: Variant Y-13323634-C-T is Benign according to our data. Variant chrY-13323634-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2595555.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd4 at 7 gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	NM_001258249.2	MANE Select	c.3197G>A	p.Arg1066His	missense	Exon 21 of 30	NP_001245178.1	F5H8B4
	UTY	NM_001400170.1		c.3041G>A	p.Arg1014His	missense	Exon 20 of 29	NP_001387099.1
	UTY	NM_001400171.1		c.2996G>A	p.Arg999His	missense	Exon 20 of 29	NP_001387100.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTY	ENST00000545955.6	TSL:1 MANE Select	c.3197G>A	p.Arg1066His	missense	Exon 21 of 30	ENSP00000442047.2	F5H8B4
	UTY	ENST00000382896.9	TSL:1	c.3131G>A	p.Arg1044His	missense	Exon 21 of 30	ENSP00000372352.5	A0A8C8KHL4
	UTY	ENST00000617789.5	TSL:1	c.3062G>A	p.Arg1021His	missense	Exon 20 of 29	ENSP00000483735.1	A0A087X0Y2

Frequencies

GnomAD3 genomes AF: 0.000211 AC: 7 AN: 33162 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000236

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000372

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000148 AC: 10 AN: 67753 AF XY: 0.000148

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000316

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000207 AC: 75 AN: 362755 Hom.: 0 Cov.: 0 AF XY: 0.000207 AC XY: 75 AN XY: 362755

African (AFR) AF: 0.000141 AC: 1 AN: 7069

American (AMR) AF: 0.000105 AC: 1 AN: 9502

Ashkenazi Jewish (ASJ) AF: 0.000149 AC: 1 AN: 6730

East Asian (EAS) AF: 0.000105 AC: 1 AN: 9482

South Asian (SAS) AF: 0.0000312 AC: 1 AN: 32076

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12878

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1627

European-Non Finnish (NFE) AF: 0.000253 AC: 68 AN: 269124

Other (OTH) AF: 0.000140 AC: 2 AN: 14267

GnomAD4 genome AF: 0.000211 AC: 7 AN: 33162 Hom.: 0 Cov.: 0 AF XY: 0.000211 AC XY: 7 AN XY: 33162

African (AFR) AF: 0.000236 AC: 2 AN: 8483

American (AMR) AF: 0.00 AC: 0 AN: 3635

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 760

East Asian (EAS) AF: 0.00 AC: 0 AN: 1281

South Asian (SAS) AF: 0.00 AC: 0 AN: 1501

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3290

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

European-Non Finnish (NFE) AF: 0.000372 AC: 5 AN: 13453

Other (OTH) AF: 0.00 AC: 0 AN: 470

ExAC AF: 0.0000287 AC: 2

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	16
DANN	Benign	0.76
DEOGEN2	Benign	0.12	T
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.77	T
M_CAP	Benign	0.045	D
MetaRNN	Benign	0.16	T
MutationAssessor	Benign	0.90	L
PhyloP100		2.4
PROVEAN	Benign	-1.7	N
Sift	Benign	0.39	T
Sift4G	Benign	0.13	T
Polyphen		0.0070	B
Vest4		0.15
MVP		0.068
GERP RS		-1.5
Varity_R		0.090
gMVP		0.55
Mutation Taster		=88/12	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: rs547367934; hg19: chrY-15435514;