rs6413429

Variant names:

• chr5-1446912-C-A
• rs6413429

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0513 AC: 2131 AN: 41546

American (AMR) AF: 0.0508 AC: 778 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.0149 AC: 77 AN: 5162

South Asian (SAS) AF: 0.0571 AC: 276 AN: 4830

European-Finnish (FIN) AF: 0.0877 AC: 930 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4476 AN: 67992

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0569 Hom.: 34

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs6413429; hg19: chr5-1447027;