Y-2800415-T-C

Variant names:

• chrY-2800415-T-C
• rs2058276
• ENST00000679518.1:n.106+25676T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000679518.1(XGY2):​n.106+25676T>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 0.66 (0 hom., 21024 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: XGY2 ENST00000679518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

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+25676T>C		intron	N/A
	XGY2	ENST00000681787.1		n.106+25676T>C		intron	N/A
	XGY2	ENST00000681940.1		n.106+25676T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 20961 AN: 31853 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.616

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.659 AC: 21024 AN: 31911 Hom.: 0 Cov.: 0 AF XY: 0.659 AC XY: 21024 AN XY: 31911

African (AFR) AF: 0.810 AC: 6614 AN: 8164

American (AMR) AF: 0.507 AC: 1749 AN: 3449

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 682 AN: 760

East Asian (EAS) AF: 0.999 AC: 1195 AN: 1196

South Asian (SAS) AF: 0.990 AC: 1360 AN: 1374

European-Finnish (FIN) AF: 0.976 AC: 2960 AN: 3033

Middle Eastern (MID) AF: 0.986 AC: 73 AN: 74

European-Non Finnish (NFE) AF: 0.458 AC: 6048 AN: 13192

Other (OTH) AF: 0.619 AC: 284 AN: 459

Alfa AF: 0.518 Hom.: 23817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2058276;

hg19: chrY-2668456;