chrY-19755427-T-C

Position:

• chrY-19755427-T-C

Variant summary

Our verdict is Likely benign. Variant got -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: ENST00000652994.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377224	XR_001756067.3	n.1371T>C		non_coding_transcript_exon_variant	3/3
LOC105377224	XR_938630.4	n.1241T>C		non_coding_transcript_exon_variant	3/3
LOC105377224	XR_007068464.1	n.1085+103T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652994.1	n.1074T>C		non_coding_transcript_exon_variant	3/3
	ENST00000653234.1	n.1371T>C		non_coding_transcript_exon_variant	3/3

Frequencies

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

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

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0437

Gnomad4 FIN AF: 0.00172

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.168

Alfa AF: 0.0919 Hom.: 3923

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032652; hg19: chrY-21917313;