rs16831128

Variant names:

• chr2-132386819-A-G
• rs16831128

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 0.196 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.196 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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.211

Alfa AF: 0.212 Hom.: 7976

Bravo AF: 0.194

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16831128; hg19: chr2-133144392;