3-128578726-G-C

Variant names:

• chr3-128578726-G-C
• rs9880192

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 0.305 in 152,098 control chromosomes in the GnomAD database, including 7,925 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 0.31 (7925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.306 AC: 46430 AN: 151978 Hom.: 7926 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.305 AC: 46423 AN: 152098 Hom.: 7925 Cov.: 32 AF XY: 0.299 AC XY: 22193 AN XY: 74342

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.305

Alfa AF: 0.351 Hom.: 1202

Bravo AF: 0.293

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9880192; hg19: chr3-128297569;