rs6413429

Positions:

• chr5-1446912-C-A

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 0.0601 in 152,220 control chromosomes in the GnomAD database, including 294 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 0.060 (294 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0642 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: 0.0601 AC: 9137 AN: 152102 Hom.: 294 Cov.: 33

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0601 AC: 9146 AN: 152220 Hom.: 294 Cov.: 33 AF XY: 0.0611 AC XY: 4549 AN XY: 74414

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.0508

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.0149

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0877

Gnomad4 NFE AF: 0.0658

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0576 Hom.: 33

Bravo AF: 0.0564

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.037
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: rs6413429; hg19: chr5-1447027;