rs429988

Variant names:

• chr3-41064574-A-G
• rs429988

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 0.626 in 151,978 control chromosomes in the GnomAD database, including 30,107 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 0.63 (30107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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: 0.626 AC: 95024 AN: 151860 Hom.: 30069 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.626 AC: 95108 AN: 151978 Hom.: 30107 Cov.: 32 AF XY: 0.616 AC XY: 45777 AN XY: 74292

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.620

Alfa AF: 0.648 Hom.: 16031

Bravo AF: 0.624

Asia WGS AF: 0.519 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs429988; hg19: chr3-41106065;