rs254682

Positions:

• chr5-157786489-A-G
• chr5-157786489-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014666.4(CLINT1):​c.*1157T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.411 in 152,318 control chromosomes in the GnomAD database, including 13,426 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 0.41 (13399 hom., cov: 32)
  • Exomes 𝑓: 0.36 (27 hom.)
• Consequence: CLINT1 NM_014666.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLINT1	NM_014666.4	c.*1157T>C		3_prime_UTR_variant	12/12	ENST00000411809.7	NP_055481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLINT1	ENST00000411809.7	c.*1157T>C		3_prime_UTR_variant	12/12	1	NM_014666.4	ENSP00000388340	A1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62478 AN: 151768 Hom.: 13391 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.359 AC: 155 AN: 432 Hom.: 27 Cov.: 0 AF XY: 0.362 AC XY: 94 AN XY: 260

Gnomad4 FIN exome AF: 0.364

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.412 AC: 62502 AN: 151886 Hom.: 13399 Cov.: 32 AF XY: 0.409 AC XY: 30374 AN XY: 74222

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.424

Alfa AF: 0.448 Hom.: 22919

Bravo AF: 0.430

Asia WGS AF: 0.498 AC: 1718 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	16
DANN	Benign	0.90

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: rs254682; hg19: chr5-157213497;