3-128449578-A-G

Variant names:

• chr3-128449578-A-G
• rs6439127

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 0.86 in 152,214 control chromosomes in the GnomAD database, including 56,801 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 0.86 (56801 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.860 AC: 130822 AN: 152096 Hom.: 56759 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.860 AC: 130924 AN: 152214 Hom.: 56801 Cov.: 32 AF XY: 0.863 AC XY: 64248 AN XY: 74440

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.868

Alfa AF: 0.873 Hom.: 7094

Bravo AF: 0.850

Asia WGS AF: 0.910 AC: 3166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6439127; hg19: chr3-128168421;