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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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 v4.9

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;