2-18368791-T-C

Variant names:

• chr2-18368791-T-C
• rs1400452

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 0.257 in 152,048 control chromosomes in the GnomAD database, including 6,110 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 0.26 (6110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38983 AN: 151930 Hom.: 6107 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.257 AC: 39018 AN: 152048 Hom.: 6110 Cov.: 33 AF XY: 0.263 AC XY: 19545 AN XY: 74330

African (AFR) AF: 0.377 AC: 15615 AN: 41464

American (AMR) AF: 0.256 AC: 3907 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3034 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10584

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10509 AN: 67964

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.191 Hom.: 13686

Bravo AF: 0.267

Asia WGS AF: 0.445 AC: 1541 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1400452; hg19: chr2-18550057;