rs254677

Variant names:

• chr5-157828475-G-A
• rs254677
• NM_014666.4:c.42-10928C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014666.4(CLINT1):​c.42-10928C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,772 control chromosomes in the GnomAD database, including 23,845 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 0.56 (23845 hom., cov: 31)
• Consequence: CLINT1 NM_014666.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLINT1	NM_014666.4	MANE Select	c.42-10928C>T		intron	N/A	NP_055481.1
	CLINT1	NM_001195555.2		c.42-10928C>T		intron	N/A	NP_001182484.1
	CLINT1	NM_001195556.2		c.-13-10928C>T		intron	N/A	NP_001182485.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLINT1	ENST00000411809.7	TSL:1 MANE Select	c.42-10928C>T		intron	N/A	ENSP00000388340.2
	CLINT1	ENST00000523908.5	TSL:1	c.42-10928C>T		intron	N/A	ENSP00000429824.1
	CLINT1	ENST00000904378.1		c.42-10928C>T		intron	N/A	ENSP00000574437.1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84211 AN: 151654 Hom.: 23822 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.555 AC: 84288 AN: 151772 Hom.: 23845 Cov.: 31 AF XY: 0.552 AC XY: 40973 AN XY: 74174

African (AFR) AF: 0.611 AC: 25261 AN: 41316

American (AMR) AF: 0.636 AC: 9698 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4053 AN: 5158

South Asian (SAS) AF: 0.552 AC: 2654 AN: 4808

European-Finnish (FIN) AF: 0.413 AC: 4335 AN: 10508

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34660 AN: 67950

Other (OTH) AF: 0.568 AC: 1200 AN: 2112

Alfa AF: 0.536 Hom.: 37746

Bravo AF: 0.580

Asia WGS AF: 0.641 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.74
PhyloP100		-0.050
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: rs254677; hg19: chr5-157255483;