2-218381926-C-CGTGT

Position:

• chr2-218381926-C-CGTGT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The variant allele was found at a frequency of 0.00433 in 185,388 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0041 (3 hom., cov: 21)
  • Exomes 𝑓: 0.0052 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 3 gene

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: 0.00412 AC: 613 AN: 148766 Hom.: 3 Cov.: 21

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00450

Gnomad ASJ AF: 0.00583

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00297

Gnomad FIN AF: 0.000302

Gnomad MID AF: 0.0194

Gnomad NFE AF: 0.000954

Gnomad OTH AF: 0.00491

GnomAD4 exome AF: 0.00520 AC: 190 AN: 36532 Hom.: 0 AF XY: 0.00503 AC XY: 98 AN XY: 19480

Gnomad4 AFR exome AF: 0.0129

Gnomad4 AMR exome AF: 0.00201

Gnomad4 ASJ exome AF: 0.00723

Gnomad4 EAS exome AF: 0.00190

Gnomad4 SAS exome AF: 0.00477

Gnomad4 FIN exome AF: 0.00410

Gnomad4 NFE exome AF: 0.00546

Gnomad4 OTH exome AF: 0.00512

GnomAD4 genome AF: 0.00411 AC: 612 AN: 148856 Hom.: 3 Cov.: 21 AF XY: 0.00393 AC XY: 285 AN XY: 72490

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.00449

Gnomad4 ASJ AF: 0.00583

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00298

Gnomad4 FIN AF: 0.000302

Gnomad4 NFE AF: 0.000954

Gnomad4 OTH AF: 0.00486

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;