18-624631-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ENSG00000288533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393344.1. 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
	CLUL1	NM_001393344.1	MANE Select	c.256-234T>G		intron	N/A	NP_001380273.1
	CLUL1	NM_001289036.3		c.256-234T>G		intron	N/A	NP_001275965.2
	CLUL1	NM_001318522.2		c.256-234T>G		intron	N/A	NP_001305451.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLUL1	ENST00000692774.1	MANE Select	c.256-234T>G		intron	N/A	ENSP00000510271.1
	CLUL1	ENST00000338387.11	TSL:1	c.256-234T>G		intron	N/A	ENSP00000341128.6
	CLUL1	ENST00000400606.6	TSL:1	c.256-234T>G		intron	N/A	ENSP00000383449.2

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

African (AFR) AF: 0.234 AC: 9681 AN: 41456

American (AMR) AF: 0.585 AC: 8927 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3155 AN: 5170

South Asian (SAS) AF: 0.623 AC: 3000 AN: 4818

European-Finnish (FIN) AF: 0.376 AC: 3965 AN: 10556

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32728 AN: 67956

Other (OTH) AF: 0.460 AC: 972 AN: 2112

Alfa AF: 0.477 Hom.: 36542

Bravo AF: 0.428

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.37
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: rs505140; hg19: chr18-624631;