rs2018314

chr2-186920283-T-C

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 0.21 in 151,088 control chromosomes in the GnomAD database, including 3,546 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 0.21 (3546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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: 0.210 AC: 31675 AN: 150978 Hom.: 3547 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.210 AC: 31684 AN: 151088 Hom.: 3546 Cov.: 32 AF XY: 0.211 AC XY: 15552 AN XY: 73880

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.214

Alfa AF: 0.201 Hom.: 362

Bravo AF: 0.218

Asia WGS AF: 0.267 AC: 927 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.3
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2018314; hg19: chr2-187785010;