rs2577284

chr2-224064695-G-A

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 0.404 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.375

Alfa AF: 0.286 Hom.: 7792

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577284; hg19: chr2-224929412;