2-221212505-C-T

Variant names:

• chr2-221212505-C-T
• rs2015298

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 0.909 in 152,260 control chromosomes in the GnomAD database, including 63,673 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 0.91 (63673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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: 0.909 AC: 138280 AN: 152142 Hom.: 63658 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.909 AC: 138345 AN: 152260 Hom.: 63673 Cov.: 32 AF XY: 0.909 AC XY: 67703 AN XY: 74454

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.916

Alfa AF: 0.972 Hom.: 67319

Bravo AF: 0.899

Asia WGS AF: 0.861 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2015298; hg19: chr2-222077225;