rs10502288

Variant names:

• chr18-631435-G-A
• rs10502288
• NM_001393344.1:c.857-1863G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-631435-G-A
• chr18-631435-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

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

LOC105371952 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CLUL1	NM_001393344.1	c.857-1863G>A		intron_variant	Intron 6 of 9	ENST00000692774.1	NP_001380273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLUL1	ENST00000692774.1	c.857-1863G>A		intron_variant	Intron 6 of 9		NM_001393344.1	ENSP00000510271.1

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

African (AFR) AF: 0.425 AC: 17589 AN: 41416

American (AMR) AF: 0.338 AC: 5164 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2427 AN: 5146

South Asian (SAS) AF: 0.384 AC: 1845 AN: 4808

European-Finnish (FIN) AF: 0.379 AC: 4008 AN: 10570

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19650 AN: 67964

Other (OTH) AF: 0.352 AC: 743 AN: 2108

Alfa AF: 0.305 Hom.: 24791

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
PhyloP100		-0.92
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: rs10502288; hg19: chr18-631435;