rs880713

Variant names:

• chr2-128374040-A-G
• rs880713

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 0.331 in 150,624 control chromosomes in the GnomAD database, including 9,878 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 0.33 (9878 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.331 AC: 49887 AN: 150508 Hom.: 9872 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.419

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.331 AC: 49894 AN: 150624 Hom.: 9878 Cov.: 32 AF XY: 0.333 AC XY: 24519 AN XY: 73594

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.356

Alfa AF: 0.396 Hom.: 9091

Bravo AF: 0.304

Asia WGS AF: 0.342 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs880713; hg19: chr2-129131614;