18-624631-T-G

Variant names:

• chr18-624631-T-G
• rs505140
• NM_001393344.1:c.256-234T>G

Variant summary

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

The NM_001393344.1(CLUL1):​c.256-234T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,004 control chromosomes in the GnomAD database, including 15,012 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 0.42 (15012 hom., cov: 32)
• Consequence: CLUL1 NM_001393344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

CLUL1 (HGNC:2096): (clusterin like 1)

ENSG00000288533 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLUL1	NM_001393344.1	c.256-234T>G		intron_variant	Intron 4 of 9	ENST00000692774.1	NP_001380273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLUL1	ENST00000692774.1	c.256-234T>G		intron_variant	Intron 4 of 9		NM_001393344.1	ENSP00000510271.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64563 AN: 151886 Hom.: 15010 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.425 AC: 64583 AN: 152004 Hom.: 15012 Cov.: 32 AF XY: 0.429 AC XY: 31843 AN XY: 74310

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.460

Alfa AF: 0.483 Hom.: 30889

Bravo AF: 0.428

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.48

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: rs505140; hg19: chr18-624631;