chr2-6459889-C-T

Variant names:

• chr2-6459889-C-T
• rs2882650

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.263 AC: 10808 AN: 41172

American (AMR) AF: 0.534 AC: 8132 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3466

East Asian (EAS) AF: 0.538 AC: 2725 AN: 5064

South Asian (SAS) AF: 0.548 AC: 2596 AN: 4738

European-Finnish (FIN) AF: 0.671 AC: 6892 AN: 10276

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31021 AN: 67802

Other (OTH) AF: 0.412 AC: 863 AN: 2096

Alfa AF: 0.442 Hom.: 2031

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2882650; hg19: chr2-6600021;