rs3873283

chr6-29965223-A-G

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 0.215 in 151,952 control chromosomes in the GnomAD database, including 3,993 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 0.22 (3993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 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: 0.215 AC: 32657 AN: 151838 Hom.: 3981 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.215 AC: 32690 AN: 151952 Hom.: 3993 Cov.: 32 AF XY: 0.216 AC XY: 16047 AN XY: 74242

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.217

Alfa AF: 0.176 Hom.: 1830

Bravo AF: 0.227

Asia WGS AF: 0.240 AC: 829 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	14
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3873283; hg19: chr6-29933000;