12-28591708-C-T

Variant names:

• chr12-28591708-C-T
• rs10843215

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 0.875 in 152,112 control chromosomes in the GnomAD database, including 58,663 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 0.87 (58663 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819

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 (NFE) allele frequency at 95% confidence interval = 0.913 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: 0.875 AC: 132947 AN: 151994 Hom.: 58614 Cov.: 30

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.875 AC: 133054 AN: 152112 Hom.: 58663 Cov.: 30 AF XY: 0.873 AC XY: 64903 AN XY: 74360

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.887

Alfa AF: 0.903 Hom.: 68953

Bravo AF: 0.858

Asia WGS AF: 0.764 AC: 2657 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	0.60
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10843215; hg19: chr12-28744641;