12-49080822-C-T

Variant names:

• chr12-49080822-C-T
• rs12821008

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 0.309 in 151,898 control chromosomes in the GnomAD database, including 8,928 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 0.31 (8928 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 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: 0.309 AC: 46928 AN: 151776 Hom.: 8930 Cov.: 31

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.309 AC: 46929 AN: 151898 Hom.: 8928 Cov.: 31 AF XY: 0.315 AC XY: 23360 AN XY: 74218

African (AFR) AF: 0.0842 AC: 3490 AN: 41432

American (AMR) AF: 0.305 AC: 4649 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1063 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2114 AN: 5152

South Asian (SAS) AF: 0.502 AC: 2423 AN: 4822

European-Finnish (FIN) AF: 0.447 AC: 4711 AN: 10528

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27326 AN: 67934

Other (OTH) AF: 0.303 AC: 639 AN: 2106

Alfa AF: 0.366 Hom.: 20452

Bravo AF: 0.282

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs12821008; hg19: chr12-49474605;