rs2882650

Positions:

• chr2-6459889-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 0.431 in 151,050 control chromosomes in the GnomAD database, including 15,130 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 0.43 (15130 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 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: 0.431 AC: 65007 AN: 150940 Hom.: 15130 Cov.: 29

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.431 AC: 65033 AN: 151050 Hom.: 15130 Cov.: 29 AF XY: 0.441 AC XY: 32505 AN XY: 73674

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.412

Alfa AF: 0.449 Hom.: 1997

Bravo AF: 0.413

Asia WGS AF: 0.555 AC: 1928 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2882650; hg19: chr2-6600021;