rs880713

Positions:

• chr2-128374040-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;