rs16826756

Variant names:

• chr2-147032717-A-G
• rs16826756

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 0.203 in 152,204 control chromosomes in the GnomAD database, including 3,778 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 0.20 (3778 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.204 AC: 30955 AN: 152086 Hom.: 3775 Cov.: 33

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.203 AC: 30952 AN: 152204 Hom.: 3778 Cov.: 33 AF XY: 0.210 AC XY: 15633 AN XY: 74400

Gnomad4 AFR AF: 0.0810

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.199

Alfa AF: 0.234 Hom.: 771

Bravo AF: 0.196

Asia WGS AF: 0.237 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16826756; hg19: chr2-147790285;