rs16948876

Variant names:

• chr16-50820507-G-A
• rs16948876

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 0.0613 in 152,232 control chromosomes in the GnomAD database, including 389 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 0.061 (389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0806 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: 0.0613 AC: 9327 AN: 152114 Hom.: 390 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0613 AC: 9326 AN: 152232 Hom.: 389 Cov.: 32 AF XY: 0.0626 AC XY: 4657 AN XY: 74444

African (AFR) AF: 0.0132 AC: 548 AN: 41540

American (AMR) AF: 0.0789 AC: 1207 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3468

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5172

South Asian (SAS) AF: 0.0393 AC: 190 AN: 4830

European-Finnish (FIN) AF: 0.114 AC: 1212 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0824 AC: 5603 AN: 68012

Other (OTH) AF: 0.0520 AC: 110 AN: 2116

Alfa AF: 0.0716 Hom.: 749

Bravo AF: 0.0565

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.58
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs16948876; hg19: chr16-50854418;