5-157838677-A-G

Variant summary

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

The NM_014666.4(CLINT1):c.41+20253T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,080 control chromosomes in the GnomAD database, including 36,092 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 0.69 (36092 hom., cov: 32)
• Consequence: CLINT1 NM_014666.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLINT1	NM_014666.4	c.41+20253T>C		intron_variant		ENST00000411809.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLINT1	ENST00000411809.7	c.41+20253T>C		intron_variant		1	NM_014666.4	A1
CLINT1	ENST00000523908.5	c.41+20253T>C		intron_variant		1		P3
CLINT1	ENST00000523094.5	c.-14+20276T>C		intron_variant		2
CLINT1	ENST00000530742.5	c.-14+20363T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104539 AN: 151962 Hom.: 36055 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.688 AC: 104634 AN: 152080 Hom.: 36092 Cov.: 32 AF XY: 0.681 AC XY: 50606 AN XY: 74352

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.699

Alfa AF: 0.684 Hom.: 4197

Bravo AF: 0.703

Asia WGS AF: 0.703 AC: 2439 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	6.0
Dann	Benign	0.79

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: rs254664; hg19: chr5-157265685;