Y-8690928-A-T

Variant names:

• chrY-8690928-A-T
• rs17250887
• ENST00000438677.2:n.445-1773T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438677.2(TTTY18):​n.445-1773T>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTTY18	ENST00000438677.2	n.445-1773T>A		intron_variant	Intron 3 of 6	1
LINC00279	ENST00000650816.1	n.1005+569A>T		intron_variant	Intron 6 of 11
LINC00279	ENST00000651700.2	n.958+569A>T		intron_variant	Intron 6 of 7

Frequencies

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

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

African (AFR) AF: 0.0551 AC: 480 AN: 8717

American (AMR) AF: 0.150 AC: 555 AN: 3692

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 300 AN: 766

East Asian (EAS) AF: 0.00234 AC: 3 AN: 1284

South Asian (SAS) AF: 0.127 AC: 191 AN: 1501

European-Finnish (FIN) AF: 0.152 AC: 520 AN: 3432

Middle Eastern (MID) AF: 0.392 AC: 29 AN: 74

European-Non Finnish (NFE) AF: 0.237 AC: 3208 AN: 13563

Other (OTH) AF: 0.222 AC: 103 AN: 465

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

Other links and lift over

dbSNP: rs17250887; hg19: chrY-8558969;