rs4574921

Variant names:

• chr9-114776054-C-T
• rs4574921

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.908 AC: 37681 AN: 41488

American (AMR) AF: 0.811 AC: 12374 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2664 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3359 AN: 5184

South Asian (SAS) AF: 0.760 AC: 3649 AN: 4804

European-Finnish (FIN) AF: 0.816 AC: 8632 AN: 10584

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50350 AN: 67976

Other (OTH) AF: 0.775 AC: 1633 AN: 2108

Alfa AF: 0.759 Hom.: 26613

Bravo AF: 0.799

Asia WGS AF: 0.769 AC: 2673 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Uncertain risk allele

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Leprosy, susceptibility to, 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.52
PhyloP100		0.25

Splicing

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

Other links and lift over

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