chr11-5145895-C-T

Position:

• chr11-5145895-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 0.307 in 151,526 control chromosomes in the GnomAD database, including 8,375 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 0.31 (8375 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5145895C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46533 AN: 151412 Hom.: 8380 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.304

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.307 AC: 46521 AN: 151526 Hom.: 8375 Cov.: 31 AF XY: 0.310 AC XY: 22950 AN XY: 74050

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.302

Alfa AF: 0.363 Hom.: 13746

Bravo AF: 0.292

Asia WGS AF: 0.328 AC: 1129 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2472523; hg19: chr11-5167125;