18-624631-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.370
Variant links:
Genes affected
CLUL1 (HGNC:2096): (clusterin like 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLUL1NM_001393344.1 linkc.256-234T>G intron_variant Intron 4 of 9 ENST00000692774.1 NP_001380273.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLUL1ENST00000692774.1 linkc.256-234T>G intron_variant Intron 4 of 9 NM_001393344.1 ENSP00000510271.1 Q15846

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64563
AN:
151886
Hom.:
15010
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.234
Gnomad4 AMR
AF:
0.585
Gnomad4 ASJ
AF:
0.475
Gnomad4 EAS
AF:
0.610
Gnomad4 SAS
AF:
0.623
Gnomad4 FIN
AF:
0.376
Gnomad4 NFE
AF:
0.482
Gnomad4 OTH
AF:
0.460
Alfa
AF:
0.483
Hom.:
30889
Bravo
AF:
0.428
Asia WGS
AF:
0.620
AC:
2156
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
1.4
DANN
Benign
0.48

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs505140; hg19: chr18-624631; API