rs10506012

Positions:

• chr12-26874268-G-A

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 0.171 in 152,062 control chromosomes in the GnomAD database, including 2,425 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 0.17 (2425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25999 AN: 151944 Hom.: 2416 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.171 AC: 26024 AN: 152062 Hom.: 2425 Cov.: 32 AF XY: 0.173 AC XY: 12830 AN XY: 74320

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0440

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.181

Alfa AF: 0.186 Hom.: 3681

Bravo AF: 0.172

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506012; hg19: chr12-27027201;