chr5-157786489-A-G

Variant names:

• chr5-157786489-A-G
• rs254682
• ENST00000524306.1:n.2703T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000524306.1(CLINT1):​n.2703T>C variant causes a non coding transcript exon 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 ENST00000524306.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68
• Publications: 9 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 -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 rank	MANE	Protein	UniProt
CLINT1	NM_014666.4	c.*1157T>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000411809.7	NP_055481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLINT1	ENST00000411809.7	c.*1157T>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_014666.4	ENSP00000388340.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.364 AC: 155 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.307 AC: 12715 AN: 41446

American (AMR) AF: 0.542 AC: 8256 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3129 AN: 5156

South Asian (SAS) AF: 0.409 AC: 1974 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3516 AN: 10532

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29957 AN: 67904

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.446 Hom.: 28220

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
PhyloP100		3.7
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: rs254682; hg19: chr5-157213497;