rs17454584

Variant names:

• chr4-122432277-A-G
• rs17454584

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 0.165 in 152,152 control chromosomes in the GnomAD database, including 2,807 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 0.17 (2807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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: 0.166 AC: 25162 AN: 152034 Hom.: 2809 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.165 AC: 25147 AN: 152152 Hom.: 2807 Cov.: 32 AF XY: 0.170 AC XY: 12635 AN XY: 74394

African (AFR) AF: 0.0390 AC: 1622 AN: 41544

American (AMR) AF: 0.129 AC: 1976 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.129 AC: 669 AN: 5188

South Asian (SAS) AF: 0.128 AC: 618 AN: 4830

European-Finnish (FIN) AF: 0.363 AC: 3831 AN: 10548

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15258 AN: 67972

Other (OTH) AF: 0.158 AC: 333 AN: 2106

Alfa AF: 0.195 Hom.: 5678

Bravo AF: 0.143

Asia WGS AF: 0.106 AC: 367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs17454584; hg19: chr4-123353432;