rs8050984

Positions:

• chr16-77580224-C-T

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 0.209 in 151,928 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31704 AN: 151810 Hom.: 3995 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.209 AC: 31733 AN: 151928 Hom.: 4004 Cov.: 31 AF XY: 0.207 AC XY: 15397 AN XY: 74266

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.187

Alfa AF: 0.174 Hom.: 510

Bravo AF: 0.219

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.079
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8050984; hg19: chr16-77614121;