2-128374040-A-G

Variant names:

• chr2-128374040-A-G
• rs880713

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 0.331 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.331 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

African (AFR) AF: 0.107 AC: 4359 AN: 40672

American (AMR) AF: 0.318 AC: 4798 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1271 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1600 AN: 5068

South Asian (SAS) AF: 0.392 AC: 1877 AN: 4792

European-Finnish (FIN) AF: 0.489 AC: 5091 AN: 10416

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.436 AC: 29610 AN: 67852

Other (OTH) AF: 0.356 AC: 742 AN: 2082

Alfa AF: 0.369 Hom.: 10714

Bravo AF: 0.304

Asia WGS AF: 0.342 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.13
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs880713; hg19: chr2-129131614;