Y-12168275-G-A

Variant names:

• chrY-12168275-G-A
• rs17269396
• ENST00000651802.1:n.712+34726C>T

Variant summary

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

The ENST00000651802.1(ENSG00000291034):​n.712+34726C>T variant causes a intron 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 0.0054 (0 hom., 175 hem., cov: 0)
• Consequence: ENSG00000291034 ENST00000651802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 2 publications found

Genes affected

ENSG00000291034 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651802.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291034	ENST00000651802.1		n.712+34726C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00536 AC: 175 AN: 32653 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.00138

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00445

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

GnomAD4 genome AF: 0.00535 AC: 175 AN: 32710 Hom.: 0 Cov.: 0 AF XY: 0.00535 AC XY: 175 AN XY: 32710

African (AFR) AF: 0.00 AC: 0 AN: 8465

American (AMR) AF: 0.00 AC: 0 AN: 3561

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 759

East Asian (EAS) AF: 0.136 AC: 171 AN: 1260

South Asian (SAS) AF: 0.00138 AC: 2 AN: 1452

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3235

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 70

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13245

Other (OTH) AF: 0.00443 AC: 2 AN: 451

Alfa AF: 0.000269 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs17269396; hg19: chrY-14288981;