11-48212805-C-T

Variant names:

• chr11-48212805-C-T
• rs11039588

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 0.078 in 151,918 control chromosomes in the GnomAD database, including 577 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 0.078 (577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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 (SAS) allele frequency at 95% confidence interval = 0.217 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: 0.0780 AC: 11846 AN: 151800 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0576

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0780 AC: 11851 AN: 151918 Hom.: 577 Cov.: 32 AF XY: 0.0802 AC XY: 5955 AN XY: 74228

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0576

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0799 Hom.: 809

Bravo AF: 0.0756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11039588; hg19: chr11-48234357;