rs11827375

Variant names:

• chr11-76597228-G-A
• rs11827375

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 0.119 in 152,174 control chromosomes in the GnomAD database, including 1,179 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 0.12 (1179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.119 AC: 18121 AN: 152056 Hom.: 1177 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00887

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.119 AC: 18128 AN: 152174 Hom.: 1179 Cov.: 32 AF XY: 0.121 AC XY: 8990 AN XY: 74374

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00889

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.100

Alfa AF: 0.112 Hom.: 1300

Bravo AF: 0.115

Asia WGS AF: 0.0610 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11827375; hg19: chr11-76308272;