rs940469

Variant names:

• chr2-218855254-C-T
• rs940469

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.177 AC: 7349 AN: 41478

American (AMR) AF: 0.185 AC: 2829 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2556 AN: 5160

South Asian (SAS) AF: 0.182 AC: 880 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10570

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12666 AN: 67982

Other (OTH) AF: 0.193 AC: 406 AN: 2108

Alfa AF: 0.194 Hom.: 2105

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs940469; hg19: chr2-219719977;