2-121067322-T-C

Variant names:

• chr2-121067322-T-C
• rs2677510

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 0.585 in 152,130 control chromosomes in the GnomAD database, including 29,422 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 0.58 (29422 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 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: 0.585 AC: 88936 AN: 152012 Hom.: 29429 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.585 AC: 88928 AN: 152130 Hom.: 29422 Cov.: 33 AF XY: 0.583 AC XY: 43349 AN XY: 74368

African (AFR) AF: 0.262 AC: 10859 AN: 41480

American (AMR) AF: 0.619 AC: 9470 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2508 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2554 AN: 5172

South Asian (SAS) AF: 0.526 AC: 2540 AN: 4828

European-Finnish (FIN) AF: 0.734 AC: 7771 AN: 10584

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50950 AN: 67990

Other (OTH) AF: 0.629 AC: 1327 AN: 2110

Alfa AF: 0.666 Hom.: 43655

Bravo AF: 0.563

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.86
DANN	Benign	0.56
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2677510; hg19: chr2-121824898;