rs5934262

chrX-15673898-T-AchrX-15673898-T-CchrX-15673898-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000650271.1(CLTRN):c.-506+1091A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.59 (13932 hom., 19684 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: CLTRN ENST00000650271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

Genes affected

CLTRN (HGNC:29437): (collectrin, amino acid transport regulator) This gene encodes a type 1 transmembrane protein that is important for trafficking amino acid transporters to the apical brush border of proximal tubules. The encoded protein binds to amino acid transporters and regulates their expression on the plasma membrane. It also plays a role in controlling insulin exocytosis by regulating formation of the SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) complex in pancreatic beta cells. The extracellular domain of the encoded protein may be cleaved and shed from the plasma membrane specifically in pancreatic beta cells. [provided by RefSeq, Jun 2013]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd at 13914 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLTRN	XM_017029680.2	c.-99+1545A>T		intron_variant
CLTRN	XM_024452411.2	c.-99+1091A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLTRN	ENST00000650271.1	c.-506+1091A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.585 AC: 64940 AN: 110991 Hom.: 13914 Cov.: 24 AF XY: 0.591 AC XY: 19627 AN XY: 33229

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.470

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.584

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.586 AC: 65020 AN: 111044 Hom.: 13932 Cov.: 24 AF XY: 0.591 AC XY: 19684 AN XY: 33292

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.590

Alfa AF: 0.312 Hom.: 1307

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5934262; hg19: chrX-15692021;