12-55676884-C-T

Variant names:

• chr12-55676884-C-T
• rs55874825

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 0.266 in 152,056 control chromosomes in the GnomAD database, including 5,649 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 (5649 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.266 AC: 40404 AN: 151936 Hom.: 5640 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.266 AC: 40433 AN: 152056 Hom.: 5649 Cov.: 33 AF XY: 0.272 AC XY: 20180 AN XY: 74308

African (AFR) AF: 0.213 AC: 8829 AN: 41480

American (AMR) AF: 0.260 AC: 3968 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1839 AN: 5178

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4826

European-Finnish (FIN) AF: 0.371 AC: 3909 AN: 10548

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

European-Non Finnish (NFE) AF: 0.273 AC: 18575 AN: 67958

Other (OTH) AF: 0.234 AC: 495 AN: 2116

Alfa AF: 0.252 Hom.: 1875

Bravo AF: 0.253

Asia WGS AF: 0.338 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.0
DANN	Benign	0.94
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs55874825; hg19: chr12-56070668;