rs16831128

Variant names:

• chr2-132386819-A-G
• rs16831128

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 0.196 in 152,062 control chromosomes in the GnomAD database, including 3,106 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 (3106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29849 AN: 151942 Hom.: 3097 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.196 AC: 29870 AN: 152062 Hom.: 3106 Cov.: 32 AF XY: 0.200 AC XY: 14843 AN XY: 74326

African (AFR) AF: 0.142 AC: 5893 AN: 41468

American (AMR) AF: 0.227 AC: 3473 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3466

East Asian (EAS) AF: 0.187 AC: 959 AN: 5140

South Asian (SAS) AF: 0.355 AC: 1710 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10588

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14374 AN: 67978

Other (OTH) AF: 0.211 AC: 444 AN: 2108

Alfa AF: 0.210 Hom.: 12522

Bravo AF: 0.194

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.64
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs16831128; hg19: chr2-133144392;