rs12424086

Variant names:

• chr12-65970729-T-C
• rs12424086

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 0.162 in 152,136 control chromosomes in the GnomAD database, including 2,563 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 0.16 (2563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 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: 0.162 AC: 24629 AN: 152018 Hom.: 2562 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0583

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.162 AC: 24634 AN: 152136 Hom.: 2563 Cov.: 32 AF XY: 0.167 AC XY: 12391 AN XY: 74370

African (AFR) AF: 0.0452 AC: 1877 AN: 41536

American (AMR) AF: 0.181 AC: 2766 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3468

East Asian (EAS) AF: 0.0585 AC: 303 AN: 5182

South Asian (SAS) AF: 0.315 AC: 1515 AN: 4812

European-Finnish (FIN) AF: 0.240 AC: 2539 AN: 10576

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14023 AN: 67984

Other (OTH) AF: 0.201 AC: 423 AN: 2106

Alfa AF: 0.192 Hom.: 10293

Bravo AF: 0.151

Asia WGS AF: 0.168 AC: 584 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.53
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs12424086; hg19: chr12-66364509;