chr2-82461856-A-C

Position:

• chr2-82461856-A-C

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 0.37 in 151,838 control chromosomes in the GnomAD database, including 12,092 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 0.37 (12092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56130 AN: 151722 Hom.: 12059 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.370 AC: 56212 AN: 151838 Hom.: 12092 Cov.: 32 AF XY: 0.362 AC XY: 26868 AN XY: 74168

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.329

Alfa AF: 0.339 Hom.: 4547

Bravo AF: 0.379

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1549582; hg19: chr2-82688980;