rs10502288

chr18-631435-G-Achr18-631435-G-T

Variant summary

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

The NM_001393344.1(CLUL1):c.857-1863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,956 control chromosomes in the GnomAD database, including 9,537 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 (9537 hom., cov: 31)
• Consequence: CLUL1 NM_001393344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

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

LOC105371952 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLUL1	NM_001393344.1	c.857-1863G>A		intron_variant		ENST00000692774.1
LOC105371952	XR_935082.4	n.3580-110C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLUL1	ENST00000692774.1	c.857-1863G>A		intron_variant			NM_001393344.1	P1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52559 AN: 151838 Hom.: 9529 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.346 AC: 52595 AN: 151956 Hom.: 9537 Cov.: 31 AF XY: 0.353 AC XY: 26203 AN XY: 74274

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.352

Alfa AF: 0.291 Hom.: 13706

Bravo AF: 0.350

Asia WGS AF: 0.423 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.64
Dann	Benign	0.59

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: rs10502288; hg19: chr18-631435;