rs16826756

Positions:

• chr2-147032717-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;