chrY-19755427-T-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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652994.1. 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
	ENSG00000288049	ENST00000652994.1		n.1074T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000288049	ENST00000653234.1		n.1371T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000288049	ENST00000766638.1		n.*132T>C		downstream_gene	N/A

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 v4.9

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;