rs2380261

Variant names:

• chr2-234732536-C-A
• rs2380261

Your query was ambiguous. Multiple possible variants found:

• chr2-234732536-C-A
• chr2-234732536-C-G
• chr2-234732536-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;