rs12292796

Positions:

• chr11-39404549-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;