rs160952

chr16-76050645-G-Achr16-76050645-G-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 0.222 in 151,960 control chromosomes in the GnomAD database, including 3,959 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 0.22 (3959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33757 AN: 151842 Hom.: 3959 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.222 AC: 33762 AN: 151960 Hom.: 3959 Cov.: 32 AF XY: 0.219 AC XY: 16299 AN XY: 74272

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.243

Alfa AF: 0.234 Hom.: 603

Bravo AF: 0.215

Asia WGS AF: 0.162 AC: 560 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	11
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs160952; hg19: chr16-76084543;