rs40457

chr8-89811459-A-G

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 0.574 in 152,024 control chromosomes in the GnomAD database, including 26,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).

• Frequency: Genomes: 𝑓 0.57 (26242 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Uncertain risk allele no assertion criteria provided O:1
• Conservation: PhyloP100: 1.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87110 AN: 151904 Hom.: 26214 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.574 AC: 87195 AN: 152024 Hom.: 26242 Cov.: 31 AF XY: 0.569 AC XY: 42287 AN XY: 74286

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.558

Alfa AF: 0.524 Hom.: 49280

Bravo AF: 0.575

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Significance: Uncertain risk allele

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Leprosy, susceptibility to, 1 Other:1

Uncertain risk allele, no assertion criteria provided

case-control

Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta

Jun 10, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	11
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs40457; hg19: chr8-90823687;