rs17661237

Variant names:

• chr22-24690849-C-G
• rs17661237

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 0.156 in 152,132 control chromosomes in the GnomAD database, including 2,005 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 0.16 (2005 hom., cov: 33)
• Consequence: ARL5AP4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 0 publications found

Genes affected

ARL5AP4 (HGNC:43936): (ARL5A pseudogene 4)

ENSG00000282012 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL5AP4		n.24690849C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282012	ENST00000748010.1	n.159-131G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23749 AN: 152014 Hom.: 2008 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.156 AC: 23752 AN: 152132 Hom.: 2005 Cov.: 33 AF XY: 0.154 AC XY: 11430 AN XY: 74366

African (AFR) AF: 0.207 AC: 8606 AN: 41484

American (AMR) AF: 0.122 AC: 1869 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3472

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5184

South Asian (SAS) AF: 0.134 AC: 644 AN: 4814

European-Finnish (FIN) AF: 0.0781 AC: 827 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10556 AN: 67992

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.152 Hom.: 246

Bravo AF: 0.161

Asia WGS AF: 0.0950 AC: 330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.32
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs17661237; hg19: chr22-25086816;