rs16981293

Variant names:

• chrY-8928037-C-T
• rs16981293

Variant summary

Our verdict is Benign. Variant got -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 0.077 (0 hom., 2552 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.0771 AC: 2552 AN: 33116 Hom.: 0 Cov.: 0 AF XY: 0.0771 AC XY: 2552 AN XY: 33116

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.0896

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0131

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0367

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

GnomAD4 genome AF: 0.0769 AC: 2552 AN: 33181 Hom.: 0 Cov.: 0 AF XY: 0.0769 AC XY: 2552 AN XY: 33181

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.0131

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.160 Hom.: 7355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16981293; hg19: chrY-8796078;