rs1858329

Variant names:

• chr12-83631335-C-G
• rs1858329

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 0.0393 in 152,222 control chromosomes in the GnomAD database, including 267 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 0.039 (267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.0393 AC: 5977 AN: 152104 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0129

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00434

Gnomad FIN AF: 0.00406

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0393 AC: 5982 AN: 152222 Hom.: 267 Cov.: 32 AF XY: 0.0382 AC XY: 2843 AN XY: 74436

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0129

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00434

Gnomad4 FIN AF: 0.00406

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0280 Hom.: 18

Bravo AF: 0.0442

Asia WGS AF: 0.00810 AC: 28 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1858329; hg19: chr12-84025114;