rs2380261

chr2-234732536-C-Achr2-234732536-C-Gchr2-234732536-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.27 in 152,082 control chromosomes in the GnomAD database, including 6,059 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 (6059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41000 AN: 151964 Hom.: 6063 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.270 AC: 41012 AN: 152082 Hom.: 6059 Cov.: 32 AF XY: 0.275 AC XY: 20423 AN XY: 74330

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.293

Alfa AF: 0.272 Hom.: 9852

Bravo AF: 0.276

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.2
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2380261; hg19: chr2-235641180; COSMIC: COSV64076426;