rs568273

Variant summary

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

The NM_001393344.1(CLUL1):​c.-14+3058A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,154 control chromosomes in the GnomAD database, including 57,863 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 0.83 ( 57863 hom., cov: 32)

Consequence

CLUL1
NM_001393344.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.518
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLUL1NM_001393344.1 linkuse as main transcriptc.-14+3058A>G intron_variant ENST00000692774.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLUL1ENST00000692774.1 linkuse as main transcriptc.-14+3058A>G intron_variant NM_001393344.1 P1

Frequencies

GnomAD3 genomes
AF:
0.835
AC:
126948
AN:
152036
Hom.:
57854
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.428
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.935
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.997
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.991
Gnomad NFE
AF:
0.998
Gnomad OTH
AF:
0.882
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.835
AC:
126984
AN:
152154
Hom.:
57863
Cov.:
32
AF XY:
0.839
AC XY:
62425
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.427
Gnomad4 AMR
AF:
0.935
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.997
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.998
Gnomad4 OTH
AF:
0.884
Alfa
AF:
0.893
Hom.:
7863
Bravo
AF:
0.812
Asia WGS
AF:
0.967
AC:
3362
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.31
DANN
Benign
0.85

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: rs568273; hg19: chr18-610157; API