chr2-549873-G-C

Variant names:

• chr2-549873-G-C
• rs2685263

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 0.522 in 151,894 control chromosomes in the GnomAD database, including 21,290 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 0.52 (21290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79229 AN: 151776 Hom.: 21256 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.522 AC: 79316 AN: 151894 Hom.: 21290 Cov.: 32 AF XY: 0.530 AC XY: 39336 AN XY: 74252

African (AFR) AF: 0.499 AC: 20647 AN: 41376

American (AMR) AF: 0.637 AC: 9725 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1479 AN: 3470

East Asian (EAS) AF: 0.872 AC: 4517 AN: 5182

South Asian (SAS) AF: 0.619 AC: 2984 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5262 AN: 10528

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33050 AN: 67944

Other (OTH) AF: 0.515 AC: 1083 AN: 2104

Alfa AF: 0.344 Hom.: 860

Bravo AF: 0.533

Asia WGS AF: 0.764 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.48
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs2685263; hg19: chr2-549873;