rs12292796

Variant names:

• chr11-39404549-A-C
• rs12292796

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.198 AC: 8225 AN: 41510

American (AMR) AF: 0.0480 AC: 734 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3472

East Asian (EAS) AF: 0.0583 AC: 301 AN: 5162

South Asian (SAS) AF: 0.161 AC: 777 AN: 4822

European-Finnish (FIN) AF: 0.0507 AC: 537 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4025 AN: 68010

Other (OTH) AF: 0.0935 AC: 197 AN: 2106

Alfa AF: 0.0811 Hom.: 254

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
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs12292796; hg19: chr11-39426099;