rs2032631

Variant names:

• chrY-19705901-A-G
• rs2032631
• NM_004653.5:c.*94T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 16 publications found

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]

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: NM_004653.5. 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
	KDM5D	NM_004653.5	MANE Select	c.*94T>C		3_prime_UTR	Exon 27 of 27	NP_004644.2
	KDM5D	NM_001146705.2		c.*94T>C		3_prime_UTR	Exon 28 of 28	NP_001140177.1	Q9BY66-3
	KDM5D	NM_001146706.2		c.*94T>C		3_prime_UTR	Exon 26 of 26	NP_001140178.1	Q9BY66-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDM5D	ENST00000317961.9	TSL:1 MANE Select	c.*94T>C		3_prime_UTR	Exon 27 of 27	ENSP00000322408.4	Q9BY66-1
	KDM5D	ENST00000541639.5	TSL:1	c.*94T>C		3_prime_UTR	Exon 28 of 28	ENSP00000444293.1	Q9BY66-3
	KDM5D	ENST00000382806.6	TSL:1	c.*94T>C		3_prime_UTR	Exon 26 of 26	ENSP00000372256.2	Q9BY66-2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 17913 AN: 31713 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.826 AC: 2805 AN: 3394

American (AMR) AF: 0.360 AC: 1722 AN: 4777

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 3072 AN: 4117

East Asian (EAS) AF: 0.990 AC: 7822 AN: 7898

South Asian (SAS) AF: 0.502 AC: 9779 AN: 19499

European-Finnish (FIN) AF: 0.910 AC: 8283 AN: 9102

Middle Eastern (MID) AF: 0.838 AC: 642 AN: 766

European-Non Finnish (NFE) AF: 0.370 AC: 35795 AN: 96744

Other (OTH) AF: 0.523 AC: 3865 AN: 7389

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

African (AFR) AF: 0.787 AC: 6308 AN: 8015

American (AMR) AF: 0.379 AC: 1339 AN: 3536

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 574 AN: 743

East Asian (EAS) AF: 0.981 AC: 1167 AN: 1189

South Asian (SAS) AF: 0.504 AC: 685 AN: 1359

European-Finnish (FIN) AF: 0.930 AC: 2817 AN: 3029

Middle Eastern (MID) AF: 0.959 AC: 70 AN: 73

European-Non Finnish (NFE) AF: 0.358 AC: 4718 AN: 13186

Other (OTH) AF: 0.548 AC: 238 AN: 434

Alfa AF: 0.436 Hom.: 18660

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.13
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism

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

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

Other links and lift over

dbSNP: rs2032631;

hg19: chrY-21867787;