11-123268909-C-T

Variant names:

• chr11-123268909-C-T
• rs4351827

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 0.234 in 151,902 control chromosomes in the GnomAD database, including 4,481 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 0.23 (4481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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: 0.234 AC: 35482 AN: 151784 Hom.: 4472 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.234 AC: 35542 AN: 151902 Hom.: 4481 Cov.: 32 AF XY: 0.236 AC XY: 17495 AN XY: 74246

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.221

Alfa AF: 0.227 Hom.: 505

Bravo AF: 0.245

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
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: rs4351827; hg19: chr11-123139617;