rs12926729

Variant names:

• chr16-20089048-G-A
• rs12926729

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 0.194 in 152,112 control chromosomes in the GnomAD database, including 3,437 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 0.19 (3437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29478 AN: 151994 Hom.: 3439 Cov.: 32

Gnomad AFR AF: 0.0602

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.194 AC: 29479 AN: 152112 Hom.: 3437 Cov.: 32 AF XY: 0.197 AC XY: 14650 AN XY: 74348

African (AFR) AF: 0.0601 AC: 2498 AN: 41532

American (AMR) AF: 0.218 AC: 3328 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5176

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4816

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10564

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16643 AN: 67948

Other (OTH) AF: 0.184 AC: 388 AN: 2112

Alfa AF: 0.170 Hom.: 1085

Bravo AF: 0.183

Asia WGS AF: 0.224 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs12926729; hg19: chr16-20100370;