rs429988

Positions:

• chr3-41064574-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 0.626 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;