5-157838677-A-G

Variant names:

• chr5-157838677-A-G
• rs254664
• NM_014666.4:c.41+20253T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014666.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLINT1	NM_014666.4	MANE Select	c.41+20253T>C		intron	N/A	NP_055481.1
	CLINT1	NM_001195555.2		c.41+20253T>C		intron	N/A	NP_001182484.1
	CLINT1	NM_001195556.2		c.-14+20276T>C		intron	N/A	NP_001182485.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLINT1	ENST00000411809.7	TSL:1 MANE Select	c.41+20253T>C		intron	N/A	ENSP00000388340.2
	CLINT1	ENST00000523908.5	TSL:1	c.41+20253T>C		intron	N/A	ENSP00000429824.1
	CLINT1	ENST00000523094.5	TSL:2	c.-14+20276T>C		intron	N/A	ENSP00000429345.1

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

African (AFR) AF: 0.674 AC: 27965 AN: 41466

American (AMR) AF: 0.745 AC: 11385 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4085 AN: 5172

South Asian (SAS) AF: 0.629 AC: 3031 AN: 4820

European-Finnish (FIN) AF: 0.576 AC: 6077 AN: 10550

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47512 AN: 68006

Other (OTH) AF: 0.699 AC: 1479 AN: 2116

Alfa AF: 0.684 Hom.: 4368

Bravo AF: 0.703

Asia WGS AF: 0.703 AC: 2439 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		-0.068
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs254664; hg19: chr5-157265685;