rs429916

chr6-33010810-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 0.121 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/exons	MANE	UniProt

Ensembl

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