rs2534636

Variant names:

• chrY-2789135-C-T
• rs2534636
• ENST00000679518.1:n.106+14396C>T

Variant summary

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

The ENST00000679518.1(XGY2):​n.106+14396C>T 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 0.062 (0 hom., 2134 hem., cov: 0)
• Consequence: XGY2 ENST00000679518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 15 publications found

Genes affected

XGY2 (HGNC:34022): (XG Y-linked 2 (pseudogene))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679518.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XGY2	ENST00000679518.1		n.106+14396C>T		intron	N/A
	XGY2	ENST00000680285.1		n.320-614C>T		intron	N/A
	XGY2	ENST00000681787.1		n.106+14396C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 2131 AN: 34370 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0188

Gnomad AMR AF: 0.00702

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.00303

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0267

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0620 AC: 2134 AN: 34433 Hom.: 0 Cov.: 0 AF XY: 0.0620 AC XY: 2134 AN XY: 34433

African (AFR) AF: 0.0190 AC: 170 AN: 8927

American (AMR) AF: 0.00701 AC: 27 AN: 3854

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 63 AN: 781

East Asian (EAS) AF: 0.00303 AC: 4 AN: 1320

South Asian (SAS) AF: 0.299 AC: 468 AN: 1567

European-Finnish (FIN) AF: 0.0364 AC: 127 AN: 3485

Middle Eastern (MID) AF: 0.0270 AC: 2 AN: 74

European-Non Finnish (NFE) AF: 0.0911 AC: 1250 AN: 13719

Other (OTH) AF: 0.0385 AC: 19 AN: 493

Alfa AF: 0.0933 Hom.: 4861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2534636; hg19: chrY-2657176;