chr9-36193491-G-T

Position:

• chr9-36193491-G-T

Variant summary

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

The NM_001833.4(CLTA):​c.217+2218G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 151,982 control chromosomes in the GnomAD database, including 917 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 0.094 (917 hom., cov: 32)
• Consequence: CLTA NM_001833.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

Genes affected

CLTA (HGNC:2090): (clathrin light chain A) Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLTA	NM_001833.4	c.217+2218G>T		intron_variant		ENST00000345519.10	NP_001824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLTA	ENST00000345519.10	c.217+2218G>T		intron_variant		1	NM_001833.4	ENSP00000242284	A1

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14336 AN: 151864 Hom.: 916 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0944 AC: 14353 AN: 151982 Hom.: 917 Cov.: 32 AF XY: 0.0949 AC XY: 7051 AN XY: 74290

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0840

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0182

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0644 Hom.: 249

Bravo AF: 0.0996

Asia WGS AF: 0.176 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.69

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: rs10972786; hg19: chr9-36193488;