rs160952

Variant names:

• chr16-76050645-G-A
• rs160952

Your query was ambiguous. Multiple possible variants found:

• chr16-76050645-G-A
• chr16-76050645-G-T

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 0.222 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.176 AC: 7287 AN: 41450

American (AMR) AF: 0.202 AC: 3079 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3464

East Asian (EAS) AF: 0.0654 AC: 339 AN: 5182

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2564 AN: 10542

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17733 AN: 67916

Other (OTH) AF: 0.243 AC: 512 AN: 2110

Alfa AF: 0.234 Hom.: 617

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs160952; hg19: chr16-76084543;