rs429916

Variant names:

• chr6-33010810-C-A
• rs429916

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 0.121 in 152,094 control chromosomes in the GnomAD database, including 1,705 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 0.12 (1705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.121 AC: 18331 AN: 151976 Hom.: 1702 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.00912

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.121 AC: 18348 AN: 152094 Hom.: 1705 Cov.: 31 AF XY: 0.113 AC XY: 8400 AN XY: 74376

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.0819

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.00934

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.0797

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0771 Hom.: 971

Bravo AF: 0.130

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.68
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs429916; hg19: chr6-32978587;