rs4574921

chr9-114776054-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 0.797 in 152,088 control chromosomes in the GnomAD database, including 48,752 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 0.80 (48752 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Uncertain risk allele no assertion criteria provided O:1
• Conservation: PhyloP100: 0.250

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 = 0.901 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: 0.797 AC: 121093 AN: 151970 Hom.: 48677 Cov.: 30

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.797 AC: 121232 AN: 152088 Hom.: 48752 Cov.: 30 AF XY: 0.800 AC XY: 59470 AN XY: 74378

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.775

Alfa AF: 0.759 Hom.: 24128

Bravo AF: 0.799

Asia WGS AF: 0.769 AC: 2673 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.4
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4574921; hg19: chr9-117538334; COSMIC: COSV60395626;