rs16948876

Variant names:

• chr16-50820507-G-A
• rs16948876

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 0.0613 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0613 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

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.0393

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0824

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0766 Hom.: 147

Bravo AF: 0.0565

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16948876; hg19: chr16-50854418;