18-644527-C-G

Variant names:

• chr18-644527-C-G
• rs2342700
• NM_001393344.1:c.1210-383C>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.1210-383C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,066 control chromosomes in the GnomAD database, including 14,899 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 0.43 (14899 hom., cov: 33)
• Consequence: CLUL1 NM_001393344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 6 publications found

Genes affected

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

LOC105371952 (HGNC:):

TYMSOS (HGNC:29553): (TYMS opposite strand RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLUL1	NM_001393344.1	c.1210-383C>G		intron_variant	Intron 8 of 9	ENST00000692774.1	NP_001380273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLUL1	ENST00000692774.1	c.1210-383C>G		intron_variant	Intron 8 of 9		NM_001393344.1	ENSP00000510271.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64932 AN: 151948 Hom.: 14888 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.427 AC: 64986 AN: 152066 Hom.: 14899 Cov.: 33 AF XY: 0.427 AC XY: 31758 AN XY: 74322

African (AFR) AF: 0.577 AC: 23910 AN: 41468

American (AMR) AF: 0.356 AC: 5431 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3562 AN: 5168

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4822

European-Finnish (FIN) AF: 0.320 AC: 3384 AN: 10566

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23840 AN: 67976

Other (OTH) AF: 0.426 AC: 901 AN: 2116

Alfa AF: 0.394 Hom.: 1517

Bravo AF: 0.437

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.47
PhyloP100		0.33
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: rs2342700; hg19: chr18-644527;