chr11-13552278-A-C

Variant names:

• chr11-13552278-A-C
• rs10500784

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 0.251 in 152,158 control chromosomes in the GnomAD database, including 5,882 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 0.25 (5882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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: 0.251 AC: 38182 AN: 152040 Hom.: 5886 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.251 AC: 38185 AN: 152158 Hom.: 5882 Cov.: 32 AF XY: 0.248 AC XY: 18461 AN XY: 74382

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.0453

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.250

Alfa AF: 0.317 Hom.: 10992

Bravo AF: 0.234

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500784; hg19: chr11-13573825;