2-180497652-C-T

Variant names:

• chr2-180497652-C-T
• rs16867321

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 0.224 in 151,974 control chromosomes in the GnomAD database, including 4,093 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 0.22 (4093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 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: 0.224 AC: 34060 AN: 151856 Hom.: 4077 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.224 AC: 34115 AN: 151974 Hom.: 4093 Cov.: 32 AF XY: 0.229 AC XY: 16976 AN XY: 74234

African (AFR) AF: 0.199 AC: 8266 AN: 41452

American (AMR) AF: 0.339 AC: 5180 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1906 AN: 5160

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4806

European-Finnish (FIN) AF: 0.208 AC: 2190 AN: 10544

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13896 AN: 67966

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.213 Hom.: 12300

Bravo AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.0
DANN	Benign	0.81
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs16867321; hg19: chr2-181362379;