chr11-23461398-C-T

Position:

• chr11-23461398-C-T

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 0.138 in 151,326 control chromosomes in the GnomAD database, including 1,726 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 0.14 (1726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20831 AN: 151216 Hom.: 1723 Cov.: 31

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.138 AC: 20844 AN: 151326 Hom.: 1726 Cov.: 31 AF XY: 0.137 AC XY: 10123 AN XY: 73908

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.163

Alfa AF: 0.176 Hom.: 2958

Bravo AF: 0.130

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12146457; hg19: chr11-23482944;