chr12-66056192-C-A

Variant names:

• chr12-66056192-C-A
• rs11836463

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 0.283 in 152,068 control chromosomes in the GnomAD database, including 6,270 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 0.28 (6270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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: 0.283 AC: 43045 AN: 151950 Hom.: 6255 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.283 AC: 43102 AN: 152068 Hom.: 6270 Cov.: 32 AF XY: 0.285 AC XY: 21181 AN XY: 74338

African (AFR) AF: 0.295 AC: 12244 AN: 41456

American (AMR) AF: 0.363 AC: 5540 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.108 AC: 556 AN: 5170

South Asian (SAS) AF: 0.359 AC: 1725 AN: 4804

European-Finnish (FIN) AF: 0.269 AC: 2847 AN: 10586

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18224 AN: 67982

Other (OTH) AF: 0.309 AC: 653 AN: 2114

Alfa AF: 0.272 Hom.: 24967

Bravo AF: 0.288

Asia WGS AF: 0.255 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.64
DANN	Benign	0.48
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11836463; hg19: chr12-66449972;