rs10515754

chr5-157806530-T-C

Variant summary

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

The NM_014666.4(CLINT1):c.696-418A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 152,280 control chromosomes in the GnomAD database, including 154 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 0.040 (154 hom., cov: 32)
• Consequence: CLINT1 NM_014666.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

Genes affected

CLINT1 (HGNC:23186): (clathrin interactor 1) This gene encodes a protein with similarity to the epsin family of endocytic adapter proteins. The encoded protein interacts with clathrin, the adapter protein AP-1 and phosphoinositides. This protein may be involved in the formation of clathrin coated vesicles and trafficking between the trans-Golgi network and endosomes. Mutations in this gene are associated with a susceptibility to schizophrenia and psychotic disorders. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLINT1	NM_014666.4	c.696-418A>G		intron_variant		ENST00000411809.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLINT1	ENST00000411809.7	c.696-418A>G		intron_variant		1	NM_014666.4	A1
CLINT1	ENST00000523908.5	c.696-418A>G		intron_variant		1		P3
CLINT1	ENST00000523094.5	c.642-418A>G		intron_variant		2
CLINT1	ENST00000530742.5	c.642-418A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6092 AN: 152162 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0400 AC: 6092 AN: 152280 Hom.: 154 Cov.: 32 AF XY: 0.0392 AC XY: 2918 AN XY: 74464

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0275

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0496 Hom.: 29

Bravo AF: 0.0343

Asia WGS AF: 0.00492 AC: 18 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.23
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515754; hg19: chr5-157233538;