rs254677

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLINT1	NM_014666.4	c.42-10928C>T		intron_variant	Intron 1 of 11	ENST00000411809.7	NP_055481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLINT1	ENST00000411809.7	c.42-10928C>T		intron_variant	Intron 1 of 11	1	NM_014666.4	ENSP00000388340.2
CLINT1	ENST00000523908.5	c.42-10928C>T		intron_variant	Intron 1 of 11	1		ENSP00000429824.1
CLINT1	ENST00000523094.5	c.-13-10928C>T		intron_variant	Intron 1 of 11	2		ENSP00000429345.1
CLINT1	ENST00000530742.5	c.-13-10928C>T		intron_variant	Intron 1 of 11	5		ENSP00000433419.1

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

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.568

Alfa AF: 0.525 Hom.: 22657

Bravo AF: 0.580

Asia WGS AF: 0.641 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.74

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: rs254677; hg19: chr5-157255483;