rs10506012

Variant names:

• chr12-26874268-G-A
• rs10506012

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 0.171 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.133 AC: 5502 AN: 41492

American (AMR) AF: 0.258 AC: 3941 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3466

East Asian (EAS) AF: 0.0440 AC: 228 AN: 5182

South Asian (SAS) AF: 0.201 AC: 967 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1807 AN: 10550

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12249 AN: 67980

Other (OTH) AF: 0.181 AC: 382 AN: 2112

Alfa AF: 0.179 Hom.: 7807

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
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs10506012; hg19: chr12-27027201;