rs16949486

Variant names:

• chr17-50913996-G-A
• rs16949486

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 0.146 in 152,070 control chromosomes in the GnomAD database, including 2,381 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 0.15 (2381 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 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: 0.146 AC: 22254 AN: 151952 Hom.: 2384 Cov.: 31

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.146 AC: 22252 AN: 152070 Hom.: 2381 Cov.: 31 AF XY: 0.159 AC XY: 11820 AN XY: 74326

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.166

Alfa AF: 0.152 Hom.: 3296

Bravo AF: 0.132

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16949486; hg19: chr17-48991357;