rs12292796

Variant names:

• chr11-39404549-A-C
• rs12292796

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 0.101 in 152,170 control chromosomes in the GnomAD database, including 1,088 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 0.10 (1088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.101 AC: 15300 AN: 152050 Hom.: 1084 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.101 AC: 15315 AN: 152170 Hom.: 1088 Cov.: 32 AF XY: 0.0999 AC XY: 7433 AN XY: 74380

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.0592

Gnomad4 OTH AF: 0.0935

Alfa AF: 0.0797 Hom.: 131

Bravo AF: 0.102

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.092
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12292796; hg19: chr11-39426099;