rs17862880

chr2-233773410-C-A

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 0.115 in 152,244 control chromosomes in the GnomAD database, including 1,301 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 0.12 (1301 hom., cov: 33)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.115 AC: 17519 AN: 152120 Hom.: 1296 Cov.: 33

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.115 AC: 17529 AN: 152238 Hom.: 1301 Cov.: 33 AF XY: 0.117 AC XY: 8700 AN XY: 74434

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.132

Alfa AF: 0.124 Hom.: 269

Bravo AF: 0.110

Asia WGS AF: 0.191 AC: 663 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.8
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17862880; hg19: chr2-234682056;