5-11922443-A-T

Variant names:

• chr5-11922443-A-T
• rs1458482

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 0.458 in 152,080 control chromosomes in the GnomAD database, including 16,532 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 0.46 (16532 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.458 AC: 69637 AN: 151960 Hom.: 16499 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.458 AC: 69716 AN: 152080 Hom.: 16532 Cov.: 33 AF XY: 0.463 AC XY: 34389 AN XY: 74326

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.439

Alfa AF: 0.422 Hom.: 1727

Bravo AF: 0.470

Asia WGS AF: 0.682 AC: 2366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458482; hg19: chr5-11922555;