chr12-28853059-T-C

Variant names:

• chr12-28853059-T-C
• rs4931109

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 0.863 in 152,092 control chromosomes in the GnomAD database, including 56,990 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 0.86 (56990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.894 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: 0.863 AC: 131225 AN: 151974 Hom.: 56956 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.863 AC: 131319 AN: 152092 Hom.: 56990 Cov.: 32 AF XY: 0.861 AC XY: 63971 AN XY: 74322

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.888

Alfa AF: 0.878 Hom.: 6857

Bravo AF: 0.856

Asia WGS AF: 0.750 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4931109; hg19: chr12-29005992;