chr2-180212022-C-T

Variant names:

• chr2-180212022-C-T
• rs13418455

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 0.29 in 151,930 control chromosomes in the GnomAD database, including 6,984 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 0.29 (6984 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 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: 0.290 AC: 44050 AN: 151810 Hom.: 6987 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.290 AC: 44040 AN: 151930 Hom.: 6984 Cov.: 32 AF XY: 0.286 AC XY: 21255 AN XY: 74260

African (AFR) AF: 0.192 AC: 7980 AN: 41468

American (AMR) AF: 0.276 AC: 4199 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1357 AN: 3466

East Asian (EAS) AF: 0.228 AC: 1172 AN: 5146

South Asian (SAS) AF: 0.168 AC: 811 AN: 4820

European-Finnish (FIN) AF: 0.316 AC: 3336 AN: 10550

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24105 AN: 67926

Other (OTH) AF: 0.315 AC: 664 AN: 2110

Alfa AF: 0.332 Hom.: 32499

Bravo AF: 0.284

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs13418455; hg19: chr2-181076749;