chr2-121067322-T-C

Position:

• chr2-121067322-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.121067322T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.629

Alfa AF: 0.723 Hom.: 34703

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2677510; hg19: chr2-121824898;