rs2420382

Variant names:

• chr2-60669605-A-C
• rs2420382

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 0.27 in 151,784 control chromosomes in the GnomAD database, including 5,913 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 0.27 (5913 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.270 AC: 40907 AN: 151666 Hom.: 5913 Cov.: 29

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.270 AC: 40920 AN: 151784 Hom.: 5913 Cov.: 29 AF XY: 0.263 AC XY: 19524 AN XY: 74212

African (AFR) AF: 0.354 AC: 14645 AN: 41340

American (AMR) AF: 0.211 AC: 3224 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3468

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5168

South Asian (SAS) AF: 0.156 AC: 750 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2249 AN: 10518

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17987 AN: 67918

Other (OTH) AF: 0.287 AC: 605 AN: 2106

Alfa AF: 0.267 Hom.: 3013

Bravo AF: 0.273

Asia WGS AF: 0.103 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs2420382; hg19: chr2-60896740;