rs2032631

Positions:

• chrY-19705901-A-G
• chrY-19705901-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004653.5(KDM5D):​c.*94T>C variant causes a 3 prime UTR 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 0.57 (0 hom., 17970 hem., cov: 0)
  • Exomes 𝑓: 0.48 (0 hom. 73785 hem.)
  • Failed GnomAD Quality Control
• Consequence: KDM5D NM_004653.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

KDM5D (HGNC:11115): (lysine demethylase 5D) This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

KDM5D (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDM5D	NM_004653.5	c.*94T>C		3_prime_UTR_variant	27/27	ENST00000317961.9	NP_004644.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KDM5D	ENST00000317961	c.*94T>C		3_prime_UTR_variant	27/27	1	NM_004653.5	ENSP00000322408.4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 17913 AN: 31713 Hom.: 0 Cov.: 0 AF XY: 0.565 AC XY: 17913 AN XY: 31713 FAILED QC

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.960

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.541

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.480 AC: 73785 AN: 153686 Hom.: 0 Cov.: 0 AF XY: 0.480 AC XY: 73785 AN XY: 153686

Gnomad4 AFR exome AF: 0.826

Gnomad4 AMR exome AF: 0.360

Gnomad4 ASJ exome AF: 0.746

Gnomad4 EAS exome AF: 0.990

Gnomad4 SAS exome AF: 0.502

Gnomad4 FIN exome AF: 0.910

Gnomad4 NFE exome AF: 0.370

Gnomad4 OTH exome AF: 0.523

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.566 AC: 17970 AN: 31773 Hom.: 0 Cov.: 0 AF XY: 0.566 AC XY: 17970 AN XY: 31773

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.548

Alfa AF: 0.392 Hom.: 11584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.13

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032631; hg19: chrY-21867787;