2-5856225-C-G

Variant names:

• chr2-5856225-C-G
• rs6432366

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 0.423 in 151,956 control chromosomes in the GnomAD database, including 14,290 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 0.42 (14290 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.423 AC: 64248 AN: 151838 Hom.: 14273 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.423 AC: 64307 AN: 151956 Hom.: 14290 Cov.: 33 AF XY: 0.419 AC XY: 31137 AN XY: 74248

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.391

Alfa AF: 0.307 Hom.: 837

Bravo AF: 0.418

Asia WGS AF: 0.326 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6432366; hg19: chr2-5996357;