rs16858996

Variant names:

• chr2-170862592-A-G
• rs16858996

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 0.103 in 152,182 control chromosomes in the GnomAD database, including 1,054 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 0.10 (1054 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 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: 0.103 AC: 15666 AN: 152064 Hom.: 1052 Cov.: 31

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0978

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

GnomAD4 genome AF: 0.103 AC: 15684 AN: 152182 Hom.: 1054 Cov.: 31 AF XY: 0.107 AC XY: 7970 AN XY: 74396

African (AFR) AF: 0.0295 AC: 1225 AN: 41540

American (AMR) AF: 0.182 AC: 2781 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1225 AN: 5164

South Asian (SAS) AF: 0.182 AC: 875 AN: 4818

European-Finnish (FIN) AF: 0.141 AC: 1496 AN: 10574

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7495 AN: 68014

Other (OTH) AF: 0.100 AC: 211 AN: 2108

Alfa AF: 0.103 Hom.: 893

Bravo AF: 0.105

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs16858996; hg19: chr2-171719102;