11-23391433-C-T

Position:

• chr11-23391433-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 0.447 in 151,812 control chromosomes in the GnomAD database, including 15,489 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 0.45 (15489 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23391433C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67783 AN: 151694 Hom.: 15471 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.447 AC: 67846 AN: 151812 Hom.: 15489 Cov.: 31 AF XY: 0.449 AC XY: 33340 AN XY: 74192

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.428

Alfa AF: 0.441 Hom.: 7013

Bravo AF: 0.434

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381722; hg19: chr11-23412979;