rs9526558

chr13-49408376-A-Gchr13-49408376-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001079670.3(CAB39L):c.-32+24942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,160 control chromosomes in the GnomAD database, including 3,880 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 0.22 (3880 hom., cov: 32)
• Consequence: CAB39L NM_001079670.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

CAB39L (HGNC:20290): (calcium binding protein 39 like) Predicted to enable protein serine/threonine kinase activator activity. Predicted to be involved in intracellular signal transduction. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAB39L	NM_001079670.3	c.-32+24942T>C		intron_variant		ENST00000409308.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAB39L	ENST00000409308.6	c.-32+24942T>C		intron_variant		1	NM_001079670.3	P1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34139 AN: 152042 Hom.: 3876 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.224 AC: 34157 AN: 152160 Hom.: 3880 Cov.: 32 AF XY: 0.224 AC XY: 16624 AN XY: 74376

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.240

Alfa AF: 0.109 Hom.: 162

Bravo AF: 0.226

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9526558; hg19: chr13-49982512;