11-48212805-C-T

Variant names:

• chr11-48212805-C-T
• rs11039588

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 0.078 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0457 AC: 1891 AN: 41404

American (AMR) AF: 0.0894 AC: 1364 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.172 AC: 890 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4810

European-Finnish (FIN) AF: 0.0576 AC: 606 AN: 10522

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5536 AN: 67960

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0812 Hom.: 1132

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11039588; hg19: chr11-48234357;