rs11827375

Positions:

• chr11-76597228-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;