chr4-48341885-C-T

Variant summary

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

The NM_020846.2(SLAIN2):​c.146C>T​(p.Pro49Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000734 in 1,361,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P49R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 7.3e-7 ( 0 hom. )

Consequence

SLAIN2
NM_020846.2 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.68
Variant links:
Genes affected
SLAIN2 (HGNC:29282): (SLAIN motif family member 2) Involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Located in centrosome and cytosol. Colocalizes with microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.17003062).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLAIN2NM_020846.2 linkc.146C>T p.Pro49Leu missense_variant Exon 1 of 8 ENST00000264313.11 NP_065897.1 Q9P270A0A024R9T6
SLAIN2XM_005248121.4 linkc.146C>T p.Pro49Leu missense_variant Exon 1 of 9 XP_005248178.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLAIN2ENST00000264313.11 linkc.146C>T p.Pro49Leu missense_variant Exon 1 of 8 1 NM_020846.2 ENSP00000264313.5 Q9P270

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.34e-7
AC:
1
AN:
1361624
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
671122
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:
9.40e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
20
DANN
Benign
0.97
DEOGEN2
Benign
0.030
T
Eigen
Benign
-0.60
Eigen_PC
Benign
-0.51
FATHMM_MKL
Benign
0.082
N
LIST_S2
Benign
0.84
T
M_CAP
Pathogenic
0.87
D
MetaRNN
Benign
0.17
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N
PrimateAI
Pathogenic
0.88
D
PROVEAN
Benign
-1.2
N
REVEL
Benign
0.065
Sift
Benign
0.051
T
Sift4G
Benign
0.21
T
Polyphen
0.0030
B
Vest4
0.11
MutPred
0.20
Loss of loop (P = 0.0288);
MVP
0.043
MPC
0.21
ClinPred
0.13
T
GERP RS
4.2
Varity_R
0.070
gMVP
0.38

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: rs963786237; hg19: chr4-48343902; API