rs940469

Variant names:

• chr2-218855254-C-T
• rs940469

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 0.193 in 152,078 control chromosomes in the GnomAD database, including 3,107 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 0.19 (3107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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: 0.193 AC: 29356 AN: 151960 Hom.: 3097 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.193 AC: 29383 AN: 152078 Hom.: 3107 Cov.: 32 AF XY: 0.194 AC XY: 14391 AN XY: 74340

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.193

Alfa AF: 0.186 Hom.: 1252

Bravo AF: 0.197

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs940469; hg19: chr2-219719977;