rs17250887

chrY-8690928-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438677.2(TTTY18):n.445-1773T>A variant causes a intron, non coding transcript change. 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 0.16 (0 hom., 5416 hem., cov: 0)
• Consequence: TTTY18 ENST00000438677.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

TTTY18 (HGNC:18842): (testis expressed transcript, Y-linked 18)

LINC00279 (HGNC:38724): (long intergenic non-protein coding RNA 279)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTTY18	ENST00000438677.2	n.445-1773T>A		intron_variant, non_coding_transcript_variant		1
LINC00279	ENST00000650816.1	n.1005+569A>T		intron_variant, non_coding_transcript_variant
LINC00279	ENST00000651700.1	n.958+569A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 5415 AN: 33645 Hom.: 0 Cov.: 0 AF XY: 0.161 AC XY: 5415 AN XY: 33645

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.161 AC: 5416 AN: 33710 Hom.: 0 Cov.: 0 AF XY: 0.161 AC XY: 5416 AN XY: 33710

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.00234

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.222

Alfa AF: 0.240 Hom.: 3496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.3
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17250887; hg19: chrY-8558969;