2-622827-T-C

Variant names:

• chr2-622827-T-C
• rs2867125

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 0.85 in 152,274 control chromosomes in the GnomAD database, including 55,150 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 0.85 (55150 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.850 AC: 129364 AN: 152156 Hom.: 55105 Cov.: 34

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.850 AC: 129465 AN: 152274 Hom.: 55150 Cov.: 34 AF XY: 0.851 AC XY: 63400 AN XY: 74460

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.848

Alfa AF: 0.827 Hom.: 118759

Bravo AF: 0.854

Asia WGS AF: 0.872 AC: 3033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2867125; hg19: chr2-622827;