rs12102586

Variant names:

• chr16-27366732-C-T
• rs12102586

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 0.113 in 152,138 control chromosomes in the GnomAD database, including 1,059 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 0.11 (1059 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.113 AC: 17204 AN: 152020 Hom.: 1054 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.113 AC: 17223 AN: 152138 Hom.: 1059 Cov.: 31 AF XY: 0.114 AC XY: 8503 AN XY: 74374

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.0724

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.106

Alfa AF: 0.102 Hom.: 341

Bravo AF: 0.118

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12102586; hg19: chr16-27378053;