ENST00000652994.1:n.1074T>C

Variant names:

• chrY-19755427-T-C
• rs2032652
• ENST00000652994.1:n.1074T>C

Variant summary

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

The ENST00000652994.1(ENSG00000288049):​n.1074T>C variant causes a non coding transcript exon 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 0.22 (0 hom., 7407 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288049 ENST00000652994.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 18 publications found

Genes affected

ENSG00000288049 (HGNC:58352):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KDM5D-DT	XR_001756067.3	n.1371T>C		non_coding_transcript_exon_variant	Exon 3 of 3
KDM5D-DT	XR_938630.4	n.1241T>C		non_coding_transcript_exon_variant	Exon 3 of 3
KDM5D-DT	XR_007068464.1	n.1085+103T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288049	ENST00000652994.1	n.1074T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000288049	ENST00000653234.1	n.1371T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000288049	ENST00000766638.1	n.*132T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.223 AC: 7352 AN: 32992 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0438

Gnomad FIN AF: 0.00172

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.170

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: 0.224 AC: 7407 AN: 33057 Hom.: 0 Cov.: 0 AF XY: 0.224 AC XY: 7407 AN XY: 33057

African (AFR) AF: 0.714 AC: 5800 AN: 8122

American (AMR) AF: 0.132 AC: 487 AN: 3690

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 186 AN: 758

East Asian (EAS) AF: 0.113 AC: 139 AN: 1225

South Asian (SAS) AF: 0.0437 AC: 66 AN: 1511

European-Finnish (FIN) AF: 0.00172 AC: 6 AN: 3484

Middle Eastern (MID) AF: 0.329 AC: 23 AN: 70

European-Non Finnish (NFE) AF: 0.0460 AC: 622 AN: 13522

Other (OTH) AF: 0.168 AC: 78 AN: 463

Alfa AF: 0.160 Hom.: 8935

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.29
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2032652; hg19: chrY-21917313;