rs16822551

Variant names:

• chr2-226716864-T-C
• rs16822551

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 0.137 in 152,178 control chromosomes in the GnomAD database, including 1,729 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 0.14 (1729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.137 AC: 20758 AN: 152060 Hom.: 1724 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.137 AC: 20798 AN: 152178 Hom.: 1729 Cov.: 32 AF XY: 0.136 AC XY: 10134 AN XY: 74400

African (AFR) AF: 0.220 AC: 9133 AN: 41500

American (AMR) AF: 0.162 AC: 2470 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3468

East Asian (EAS) AF: 0.170 AC: 877 AN: 5164

South Asian (SAS) AF: 0.165 AC: 794 AN: 4808

European-Finnish (FIN) AF: 0.0641 AC: 680 AN: 10616

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5985 AN: 68018

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.149 Hom.: 510

Bravo AF: 0.151

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs16822551; hg19: chr2-227581580;