rs12102586

Positions:

• chr16-27366732-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;