chr2-203820112-T-C

Variant names:

• chr2-203820112-T-C
• rs1018361

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 0.212 in 152,140 control chromosomes in the GnomAD database, including 3,849 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 (3849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32205 AN: 152022 Hom.: 3853 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.212 AC: 32225 AN: 152140 Hom.: 3849 Cov.: 32 AF XY: 0.213 AC XY: 15819 AN XY: 74402

African (AFR) AF: 0.247 AC: 10243 AN: 41484

American (AMR) AF: 0.185 AC: 2826 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2710 AN: 5162

South Asian (SAS) AF: 0.157 AC: 755 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1626 AN: 10598

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12639 AN: 67990

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.192 Hom.: 12499

Bravo AF: 0.220

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.69
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1018361; hg19: chr2-204684835;