22-24689406-C-T

Variant names:

• chr22-24689406-C-T
• rs6004238

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 0.58 in 152,042 control chromosomes in the GnomAD database, including 25,901 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 0.58 (25901 hom., cov: 33)
• Consequence: ARL5AP4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL5AP4		n.24689406C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88153 AN: 151924 Hom.: 25874 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.580 AC: 88232 AN: 152042 Hom.: 25901 Cov.: 33 AF XY: 0.581 AC XY: 43166 AN XY: 74322

African (AFR) AF: 0.669 AC: 27762 AN: 41490

American (AMR) AF: 0.587 AC: 8967 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2996 AN: 5176

South Asian (SAS) AF: 0.683 AC: 3293 AN: 4818

European-Finnish (FIN) AF: 0.506 AC: 5333 AN: 10546

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36164 AN: 67950

Other (OTH) AF: 0.576 AC: 1214 AN: 2108

Alfa AF: 0.545 Hom.: 2824

Bravo AF: 0.589

Asia WGS AF: 0.629 AC: 2177 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.84
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6004238; hg19: chr22-25085373;