rs12280753

Positions:

• chr11-116742944-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 0.131 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;