rs16947058

Variant names:

• chr17-47747820-G-A
• rs16947058

Your query was ambiguous. Multiple possible variants found:

• chr17-47747820-G-A
• chr17-47747820-G-C
• chr17-47747820-G-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 0.405 in 141,904 control chromosomes in the GnomAD database, including 11,869 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 0.41 (11869 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.405 AC: 57475 AN: 141814 Hom.: 11855 Cov.: 22

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.480

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.405 AC: 57511 AN: 141904 Hom.: 11869 Cov.: 22 AF XY: 0.398 AC XY: 27322 AN XY: 68682

African (AFR) AF: 0.433 AC: 16281 AN: 37596

American (AMR) AF: 0.345 AC: 4844 AN: 14038

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1338 AN: 3390

East Asian (EAS) AF: 0.193 AC: 965 AN: 5002

South Asian (SAS) AF: 0.414 AC: 1848 AN: 4464

European-Finnish (FIN) AF: 0.354 AC: 3076 AN: 8690

Middle Eastern (MID) AF: 0.478 AC: 131 AN: 274

European-Non Finnish (NFE) AF: 0.425 AC: 27864 AN: 65626

Other (OTH) AF: 0.398 AC: 780 AN: 1962

Alfa AF: 0.427 Hom.: 39933

Bravo AF: 0.420

Asia WGS AF: 0.320 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.31
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs16947058; hg19: chr17-45825186;