2-214696828-C-T

Variant names:

• chr2-214696828-C-T
• rs12615863

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 0.781 in 151,660 control chromosomes in the GnomAD database, including 46,312 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 0.78 (46312 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.781 AC: 118304 AN: 151542 Hom.: 46277 Cov.: 29

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.781 AC: 118390 AN: 151660 Hom.: 46312 Cov.: 29 AF XY: 0.785 AC XY: 58206 AN XY: 74124

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.750

Alfa AF: 0.781 Hom.: 16382

Bravo AF: 0.777

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12615863; hg19: chr2-215561552; COSMIC: COSV57130643;