rs2854386

Positions:

• chr2-218162779-G-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 0.865 in 152,524 control chromosomes in the GnomAD database, including 57,912 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 0.86 (57807 hom., cov: 34)
  • Exomes 𝑓: 0.92 (105 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131621 AN: 152158 Hom.: 57775 Cov.: 34

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.891

GnomAD4 exome AF: 0.919 AC: 228 AN: 248 Hom.: 105 AF XY: 0.917 AC XY: 132 AN XY: 144

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.935

Gnomad4 FIN exome AF: 0.948

Gnomad4 NFE exome AF: 0.909

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.865 AC: 131704 AN: 152276 Hom.: 57807 Cov.: 34 AF XY: 0.863 AC XY: 64299 AN XY: 74478

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.893

Alfa AF: 0.895 Hom.: 7637

Bravo AF: 0.853

Asia WGS AF: 0.880 AC: 3060 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2854386; hg19: chr2-219027502;