rs899435

Variant names:

• chr12-13299846-C-A
• rs899435

Your query was ambiguous. Multiple possible variants found:

• chr12-13299846-C-A
• chr12-13299846-C-G
• chr12-13299846-C-T

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 0.531 in 152,062 control chromosomes in the GnomAD database, including 21,941 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 0.53 (21941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.531 AC: 80722 AN: 151944 Hom.: 21932 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.531 AC: 80756 AN: 152062 Hom.: 21941 Cov.: 33 AF XY: 0.524 AC XY: 38997 AN XY: 74356

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.544

Alfa AF: 0.379 Hom.: 957

Bravo AF: 0.529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899435; hg19: chr12-13452780;