chrY-5102713-A-G

Variant names:

• chrY-5102713-A-G
• rs2571670
• NM_001395587.1:c.2853+2006A>G

Variant summary

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

The NM_001395587.1(PCDH11Y):​c.2853+2006A>G 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: not found (cov: 0)
• Consequence: PCDH11Y NM_001395587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 publications found

Genes affected

PCDH11Y (HGNC:15813): (protocadherin 11 Y-linked) This gene belongs to the protocadherin family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing seven cadherin repeats, a transmembrane domain, and a cytoplasmic tail that differs from those of the classical cadherins. This gene is located on the Y chromosome in a block of X/Y homology and is very closely related to its paralog on the X chromosome. The protein is thought to play a role in cell-cell recognition during development of the central nervous system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395587.1. 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
	PCDH11Y	NM_001395587.1	MANE Select	c.2853+2006A>G		intron	N/A	NP_001382516.1
	PCDH11Y	NM_032973.2		c.3129+2006A>G		intron	N/A	NP_116755.1
	PCDH11Y	NM_032972.3		c.3130-1631A>G		intron	N/A	NP_116754.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH11Y	ENST00000698851.1	MANE Select	c.2853+2006A>G		intron	N/A	ENSP00000513983.1
	PCDH11Y	ENST00000400457.3	TSL:1	c.3129+2006A>G		intron	N/A	ENSP00000383306.3
	PCDH11Y	ENST00000362095.9	TSL:1	c.3130-1631A>G		intron	N/A	ENSP00000355419.5

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.19
DANN	Benign	0.60
PhyloP100		-2.1

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: rs2571670; hg19: chrY-4970754;