chr2-186920283-T-C

Variant names:

• chr2-186920283-T-C
• rs2018314

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 0.21 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.183 AC: 7416 AN: 40504

American (AMR) AF: 0.317 AC: 4843 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3472

East Asian (EAS) AF: 0.171 AC: 881 AN: 5160

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4818

European-Finnish (FIN) AF: 0.129 AC: 1361 AN: 10582

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13972 AN: 67984

Other (OTH) AF: 0.214 AC: 453 AN: 2112

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2018314; hg19: chr2-187785010;