rs16947058

Positions:

• chr17-47747820-G-A
• chr17-47747820-G-C
• chr17-47747820-G-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 0.405 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.398

Alfa AF: 0.427 Hom.: 23499

Bravo AF: 0.420

Asia WGS AF: 0.320 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16947058; hg19: chr17-45825186;