rs4798418

Variant names:

• chr18-612753-T-C
• rs4798418
• NM_001393344.1:c.-13-5235T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393344.1(CLUL1):​c.-13-5235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,108 control chromosomes in the GnomAD database, including 9,518 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 0.35 (9514 hom., cov: 33)
  • Exomes 𝑓: 0.53 (4 hom.)
• Consequence: CLUL1 NM_001393344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 4 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLUL1	NM_001393344.1	c.-13-5235T>C		intron_variant	Intron 2 of 9	ENST00000692774.1	NP_001380273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLUL1	ENST00000692774.1	c.-13-5235T>C		intron_variant	Intron 2 of 9		NM_001393344.1	ENSP00000510271.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53046 AN: 151954 Hom.: 9497 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.343

GnomAD4 exome AF: 0.528 AC: 19 AN: 36 Hom.: 4 Cov.: 0 AF XY: 0.450 AC XY: 9 AN XY: 20

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 12 AN: 24

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.349 AC: 53108 AN: 152072 Hom.: 9514 Cov.: 33 AF XY: 0.351 AC XY: 26096 AN XY: 74324

African (AFR) AF: 0.358 AC: 14868 AN: 41490

American (AMR) AF: 0.387 AC: 5918 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3059 AN: 5180

South Asian (SAS) AF: 0.229 AC: 1106 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3689 AN: 10550

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22369 AN: 67962

Other (OTH) AF: 0.339 AC: 716 AN: 2112

Alfa AF: 0.336 Hom.: 19892

Bravo AF: 0.360

Asia WGS AF: 0.374 AC: 1296 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	0.67
DANN	Benign	0.20
PhyloP100		-1.1
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: rs4798418; hg19: chr18-612753;