rs406589

Positions:

• chr3-41083822-G-T

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 0.451 in 151,958 control chromosomes in the GnomAD database, including 16,049 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 0.45 (16049 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68497 AN: 151838 Hom.: 16042 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.451 AC: 68535 AN: 151958 Hom.: 16049 Cov.: 33 AF XY: 0.458 AC XY: 34017 AN XY: 74278

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.457

Alfa AF: 0.443 Hom.: 2480

Bravo AF: 0.456

Asia WGS AF: 0.607 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs406589; hg19: chr3-41125313;