rs2124029676

Variant names:

• chrY-25271643-A-C
• rs2124029676

Your query was ambiguous. Multiple possible variants found:

• chrY-25271643-A-C
• chrY-25271643-A-G
• chrY-25271643-A-T

Variant summary

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

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 0.0 (0 hom., 0 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: RBMY2YP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.919
• Publications: 2 publications found

Genes affected

RBMY2YP (HGNC:23902): (RNA binding motif protein Y-linked family 2 member Y, pseudogene)

ENSG00000306715 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423333.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBMY2YP	ENST00000423333.1	TSL:6	n.398-880A>C		intron	N/A
	ENSG00000306715	ENST00000820371.1		n.100-4307A>C		intron	N/A
	ENSG00000306715	ENST00000820372.1		n.69-4307A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 990 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

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: 0.00

Gnomad OTH AF: 0.00

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: AC0 AF: 0.00 AC: 0 AN: 990 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 990

African (AFR) AF: 0.00 AC: 0 AN: 140

American (AMR) AF: 0.00 AC: 0 AN: 87

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22

East Asian (EAS) AF: 0.00 AC: 0 AN: 82

South Asian (SAS) AF: 0.00 AC: 0 AN: 25

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 607

Other (OTH) AF: 0.00 AC: 0 AN: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.0
DANN	Benign	0.21
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs2124029676; hg19: chrY-27417790;