rs16981293

Variant names:

• chrY-8928037-C-T
• rs16981293

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 0.077 (0 hom., 2552 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0458 AC: 390 AN: 8511

American (AMR) AF: 0.0262 AC: 97 AN: 3704

Ashkenazi Jewish (ASJ) AF: 0.0131 AC: 10 AN: 761

East Asian (EAS) AF: 0.00 AC: 0 AN: 1234

South Asian (SAS) AF: 0.00 AC: 0 AN: 1457

European-Finnish (FIN) AF: 0.0106 AC: 36 AN: 3389

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 72

European-Non Finnish (NFE) AF: 0.148 AC: 1983 AN: 13375

Other (OTH) AF: 0.0365 AC: 17 AN: 466

Alfa AF: 0.160 Hom.: 9394

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs16981293; hg19: chrY-8796078;