rs12280753

Variant names:

• chr11-116742944-C-T
• rs12280753

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 0.131 in 152,114 control chromosomes in the GnomAD database, including 1,912 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 0.13 (1912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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: 0.130 AC: 19833 AN: 151996 Hom.: 1903 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.131 AC: 19876 AN: 152114 Hom.: 1912 Cov.: 32 AF XY: 0.129 AC XY: 9592 AN XY: 74382

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0902

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0496

Gnomad4 FIN AF: 0.0607

Gnomad4 NFE AF: 0.0744

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0815 Hom.: 760

Bravo AF: 0.143

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12280753; hg19: chr11-116613660;