rs11826048

Variant names:

• chr11-103527569-C-T
• rs11826048

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 0.0962 in 152,098 control chromosomes in the GnomAD database, including 722 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 0.096 (722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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: 0.0961 AC: 14600 AN: 151980 Hom.: 716 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0962 AC: 14628 AN: 152098 Hom.: 722 Cov.: 32 AF XY: 0.0971 AC XY: 7221 AN XY: 74344

Gnomad4 AFR AF: 0.0979

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0437

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0922 Hom.: 117

Bravo AF: 0.0965

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11826048; hg19: chr11-103398297;