chr2-218381926-C-CGT

Position:

• chr2-218381926-C-CGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.24 in 184,466 control chromosomes in the GnomAD database, including 4,890 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (4691 hom., cov: 21)
  • Exomes 𝑓: 0.20 (199 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37104 AN: 148560 Hom.: 4687 Cov.: 21

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.199 AC: 7116 AN: 35818 Hom.: 199 AF XY: 0.195 AC XY: 3725 AN XY: 19074

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.214

Gnomad4 ASJ exome AF: 0.195

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.151

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.250 AC: 37122 AN: 148648 Hom.: 4691 Cov.: 21 AF XY: 0.251 AC XY: 18180 AN XY: 72376

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34448891; hg19: chr2-219246649;