chr9-105468304-C-A

Variant summary

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

The NM_001145313.3(FSD1L):​c.319C>A​(p.Arg107Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000747 in 1,338,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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. R107C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.5e-7 ( 0 hom. )

Consequence

FSD1L
NM_001145313.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.75
Variant links:
Genes affected
FSD1L (HGNC:13753): (fibronectin type III and SPRY domain containing 1 like) Predicted to be located in cytoplasm. Predicted to be integral component of membrane. [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=0.09827098).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FSD1LNM_001145313.3 linkc.319C>A p.Arg107Ser missense_variant Exon 4 of 14 ENST00000481272.6 NP_001138785.1 Q9BXM9-1Q8N450

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FSD1LENST00000481272.6 linkc.319C>A p.Arg107Ser missense_variant Exon 4 of 14 2 NM_001145313.3 ENSP00000417492.1 Q9BXM9-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.47e-7
AC:
1
AN:
1338258
Hom.:
0
Cov.:
28
AF XY:
0.00000152
AC XY:
1
AN XY:
658296
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000423
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
21
DANN
Uncertain
0.98
DEOGEN2
Benign
0.013
.;.;.;T;T;T
Eigen
Benign
-0.14
Eigen_PC
Benign
0.094
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Uncertain
0.86
D;D;D;D;D;D
M_CAP
Benign
0.0059
T
MetaRNN
Benign
0.098
T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.1
.;.;.;L;.;.
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-1.3
N;N;.;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.50
T;T;.;T;T;T
Sift4G
Benign
0.28
T;T;T;T;T;T
Polyphen
0.29, 0.010, 0.0020
.;.;B;B;.;B
Vest4
0.27
MutPred
0.34
Gain of phosphorylation at R107 (P = 0.0909);.;.;Gain of phosphorylation at R107 (P = 0.0909);.;.;
MVP
0.27
ClinPred
0.46
T
GERP RS
6.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.24
gMVP
0.42

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: chr9-108230585; API