rs16949053

Variant names:

• chr17-50412079-C-T
• rs16949053

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 0.194 in 152,100 control chromosomes in the GnomAD database, including 3,222 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 (3222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 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: 29398 AN: 151982 Hom.: 3215 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.194 AC: 29432 AN: 152100 Hom.: 3222 Cov.: 32 AF XY: 0.189 AC XY: 14048 AN XY: 74378

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.250

Alfa AF: 0.203 Hom.: 1590

Bravo AF: 0.208

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16949053; hg19: chr17-48489440;