rs16947078

Variant names:

• chr17-47748134-A-G
• rs16947078

Your query was ambiguous. Multiple possible variants found:

• chr17-47748134-A-G
• chr17-47748134-A-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 0.193 in 151,546 control chromosomes in the GnomAD database, including 3,027 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 0.19 (3027 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 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: 0.193 AC: 29263 AN: 151430 Hom.: 3031 Cov.: 30

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.193 AC: 29268 AN: 151546 Hom.: 3027 Cov.: 30 AF XY: 0.187 AC XY: 13891 AN XY: 74090

African (AFR) AF: 0.197 AC: 8142 AN: 41270

American (AMR) AF: 0.167 AC: 2534 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 799 AN: 3466

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5174

South Asian (SAS) AF: 0.150 AC: 722 AN: 4800

European-Finnish (FIN) AF: 0.166 AC: 1742 AN: 10488

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14561 AN: 67842

Other (OTH) AF: 0.199 AC: 417 AN: 2100

Alfa AF: 0.213 Hom.: 4670

Bravo AF: 0.196

Asia WGS AF: 0.0840 AC: 295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.48
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs16947078; hg19: chr17-45825500;