rs16969966

Positions:

• chr17-47241086-C-A
• chr17-47241086-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.164 in 151,972 control chromosomes in the GnomAD database, including 2,403 homozygotes. 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 (2403 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24878 AN: 151854 Hom.: 2392 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.164 AC: 24930 AN: 151972 Hom.: 2403 Cov.: 31 AF XY: 0.162 AC XY: 12008 AN XY: 74290

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0914

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.158

Alfa AF: 0.126 Hom.: 737

Bravo AF: 0.170

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.059
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16969966; hg19: chr17-45318452;