rs16969966

Variant names:

• chr17-47241086-C-A
• rs16969966

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.246 AC: 10174 AN: 41384

American (AMR) AF: 0.113 AC: 1728 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5168

South Asian (SAS) AF: 0.196 AC: 942 AN: 4810

European-Finnish (FIN) AF: 0.0976 AC: 1032 AN: 10570

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8939 AN: 67978

Other (OTH) AF: 0.158 AC: 333 AN: 2110

Alfa AF: 0.129 Hom.: 864

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs16969966; hg19: chr17-45318452;