rs150587796

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001286275.2(KIAA1586):​c.-86C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,796 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

KIAA1586
NM_001286275.2 5_prime_UTR_premature_start_codon_gain

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.65
Variant links:
Genes affected
KIAA1586 (HGNC:21360): (KIAA1586) Enables SUMO ligase activity. Involved in protein sumoylation. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18295929).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIAA1586NM_020931.4 linkc.116C>G p.Ser39Trp missense_variant Exon 3 of 4 ENST00000370733.5 NP_065982.1 Q9HCI6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIAA1586ENST00000370733.5 linkc.116C>G p.Ser39Trp missense_variant Exon 3 of 4 1 NM_020931.4 ENSP00000359768.4 Q9HCI6-1
KIAA1586ENST00000545356.5 linkc.106-1902C>G intron_variant Intron 2 of 2 2 ENSP00000445507.1 F5H2N6
KIAA1586ENST00000488682.1 linkn.270C>G non_coding_transcript_exon_variant Exon 3 of 4 3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1459796
Hom.:
0
Cov.:
29
AF XY:
0.00000138
AC XY:
1
AN XY:
726378
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
6.9
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0024
T
Eigen
Benign
-0.59
Eigen_PC
Benign
-0.79
FATHMM_MKL
Benign
0.034
N
LIST_S2
Uncertain
0.90
D
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.18
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.55
N
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-0.10
N
REVEL
Benign
0.068
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.010
D
Polyphen
0.99
D
Vest4
0.41
MutPred
0.33
Loss of disorder (P = 4e-04);
MVP
0.16
MPC
0.27
ClinPred
0.62
D
GERP RS
-0.78
Varity_R
0.074
gMVP
0.030

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-56915582; API