rs16832956

Variant names:

• chr3-122298661-C-G
• rs16832956

Your query was ambiguous. Multiple possible variants found:

• chr3-122298661-C-G
• chr3-122298661-C-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 0.189 in 151,912 control chromosomes in the GnomAD database, including 2,839 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 0.19 (2839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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: 0.189 AC: 28698 AN: 151794 Hom.: 2833 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.189 AC: 28718 AN: 151912 Hom.: 2839 Cov.: 32 AF XY: 0.190 AC XY: 14124 AN XY: 74220

African (AFR) AF: 0.178 AC: 7382 AN: 41404

American (AMR) AF: 0.174 AC: 2663 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3470

East Asian (EAS) AF: 0.0510 AC: 264 AN: 5178

South Asian (SAS) AF: 0.226 AC: 1086 AN: 4800

European-Finnish (FIN) AF: 0.224 AC: 2349 AN: 10504

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13303 AN: 67970

Other (OTH) AF: 0.214 AC: 452 AN: 2114

Alfa AF: 0.199 Hom.: 394

Bravo AF: 0.184

Asia WGS AF: 0.167 AC: 581 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.83
DANN	Benign	0.82
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs16832956; hg19: chr3-122017508;