chrY-18672817-C-G

Variant names:

• chrY-18672817-C-G
• rs17250114

Variant summary

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

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 0.070 (0 hom., 2331 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 2331 AN: 33045 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.0282

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.00262

Gnomad EAS AF: 0.000794

Gnomad SAS AF: 0.000690

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0519

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

GnomAD4 genome AF: 0.0704 AC: 2331 AN: 33108 Hom.: 0 Cov.: 0 AF XY: 0.0704 AC XY: 2331 AN XY: 33108

African (AFR) AF: 0.0258 AC: 219 AN: 8482

American (AMR) AF: 0.0225 AC: 82 AN: 3648

Ashkenazi Jewish (ASJ) AF: 0.00262 AC: 2 AN: 764

East Asian (EAS) AF: 0.000795 AC: 1 AN: 1258

South Asian (SAS) AF: 0.000689 AC: 1 AN: 1452

European-Finnish (FIN) AF: 0.145 AC: 484 AN: 3329

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.113 AC: 1512 AN: 13423

Other (OTH) AF: 0.0515 AC: 24 AN: 466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs17250114; hg19: chrY-20834703;