rs1182933

Variant names:

• chr12-121016819-C-T
• rs1182933

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 0.267 in 152,120 control chromosomes in the GnomAD database, including 6,417 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 0.27 (6417 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 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: 0.267 AC: 40634 AN: 152000 Hom.: 6414 Cov.: 33

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.267 AC: 40633 AN: 152120 Hom.: 6417 Cov.: 33 AF XY: 0.275 AC XY: 20424 AN XY: 74372

African (AFR) AF: 0.0995 AC: 4132 AN: 41522

American (AMR) AF: 0.342 AC: 5233 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3472

East Asian (EAS) AF: 0.490 AC: 2538 AN: 5178

South Asian (SAS) AF: 0.398 AC: 1920 AN: 4820

European-Finnish (FIN) AF: 0.322 AC: 3399 AN: 10572

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20608 AN: 67956

Other (OTH) AF: 0.313 AC: 660 AN: 2110

Alfa AF: 0.286 Hom.: 12588

Bravo AF: 0.261

Asia WGS AF: 0.421 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		0.28
PromoterAI		0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1182933; hg19: chr12-121454622;