2-121185781-C-T

Variant names:

• chr2-121185781-C-T
• rs12467309

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 0.364 in 152,160 control chromosomes in the GnomAD database, including 12,101 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 0.36 (12101 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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: 0.365 AC: 55421 AN: 152042 Hom.: 12085 Cov.: 34

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.364 AC: 55448 AN: 152160 Hom.: 12101 Cov.: 34 AF XY: 0.373 AC XY: 27737 AN XY: 74376

African (AFR) AF: 0.126 AC: 5223 AN: 41542

American (AMR) AF: 0.507 AC: 7747 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2620 AN: 5162

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4820

European-Finnish (FIN) AF: 0.533 AC: 5640 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30150 AN: 67988

Other (OTH) AF: 0.376 AC: 794 AN: 2112

Alfa AF: 0.418 Hom.: 10807

Bravo AF: 0.356

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.73
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs12467309; hg19: chr2-121943357; COSMIC: COSV71559910;