13-49414322-T-C

Variant names:

• chr13-49414322-T-C
• rs7328100
• NM_001079670.3:c.-32+18996A>G

Variant summary

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

The NM_001079670.3(CAB39L):​c.-32+18996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,206 control chromosomes in the GnomAD database, including 58,069 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 0.87 (58069 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CAB39L NM_001079670.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAB39L	NM_001079670.3	c.-32+18996A>G		intron_variant	Intron 3 of 10	ENST00000409308.6	NP_001073138.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAB39L	ENST00000409308.6	c.-32+18996A>G		intron_variant	Intron 3 of 10	1	NM_001079670.3	ENSP00000386375.1
CAB39L	ENST00000410043.5	c.-169-13052A>G		intron_variant	Intron 3 of 11	1		ENSP00000386328.1
CAB39L	ENST00000413278.5	c.-99+6004A>G		intron_variant	Intron 1 of 4	4		ENSP00000404028.1
CAB39L	ENST00000470410.1	n.294-123A>G		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132430 AN: 152088 Hom.: 58021 Cov.: 32

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.871 AC: 132534 AN: 152206 Hom.: 58069 Cov.: 32 AF XY: 0.871 AC XY: 64839 AN XY: 74402

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.859

Alfa AF: 0.837 Hom.: 30105

Bravo AF: 0.875

Asia WGS AF: 0.862 AC: 2988 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7328100; hg19: chr13-49988458;