rs2577284

Variant names:

• chr2-224064695-G-A
• rs2577284

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 0.404 in 152,010 control chromosomes in the GnomAD database, including 15,726 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 0.40 (15726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.403 AC: 61248 AN: 151892 Hom.: 15662 Cov.: 33

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.404 AC: 61378 AN: 152010 Hom.: 15726 Cov.: 33 AF XY: 0.402 AC XY: 29883 AN XY: 74286

African (AFR) AF: 0.732 AC: 30354 AN: 41472

American (AMR) AF: 0.331 AC: 5055 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3466

East Asian (EAS) AF: 0.471 AC: 2436 AN: 5170

South Asian (SAS) AF: 0.315 AC: 1512 AN: 4804

European-Finnish (FIN) AF: 0.285 AC: 3007 AN: 10540

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16700 AN: 67972

Other (OTH) AF: 0.375 AC: 791 AN: 2112

Alfa AF: 0.302 Hom.: 11453

Bravo AF: 0.423

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.73
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2577284; hg19: chr2-224929412;