chr10-102597221-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_016169.4(SUFU):​c.838C>G​(p.Arg280Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: 32)

Consequence

SUFU
NM_016169.4 missense

Scores

1
6
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.72
Variant links:
Genes affected
SUFU (HGNC:16466): (SUFU negative regulator of hedgehog signaling) The Hedgehog signaling pathway plays an important role in early human development. The pathway is a signaling cascade that plays a role in pattern formation and cellular proliferation during development. This gene encodes a negative regulator of the hedgehog signaling pathway. Defects in this gene are a cause of medulloblastoma. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39088959).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SUFUNM_016169.4 linkc.838C>G p.Arg280Gly missense_variant 7/12 ENST00000369902.8 NP_057253.2 Q9UMX1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SUFUENST00000369902.8 linkc.838C>G p.Arg280Gly missense_variant 7/121 NM_016169.4 ENSP00000358918.4 Q9UMX1-1
SUFUENST00000423559.2 linkc.838C>G p.Arg280Gly missense_variant 7/101 ENSP00000411597.2 Q9UMX1-3
SUFUENST00000369899.6 linkc.838C>G p.Arg280Gly missense_variant 7/111 ENSP00000358915.2 Q9UMX1-2
SUFUENST00000471000.1 linkn.620C>G non_coding_transcript_exon_variant 5/65

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.33
BayesDel_addAF
Uncertain
0.037
T
BayesDel_noAF
Benign
-0.18
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.19
T;.;.
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.42
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
0.98
D;D;D
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.39
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.0
L;L;L
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
-1.1
N;N;N
REVEL
Benign
0.18
Sift
Benign
0.046
D;T;T
Sift4G
Benign
0.20
T;T;T
Polyphen
0.12
B;B;P
Vest4
0.72
MutPred
0.40
Gain of glycosylation at S279 (P = 0.0407);Gain of glycosylation at S279 (P = 0.0407);Gain of glycosylation at S279 (P = 0.0407);
MVP
0.20
MPC
0.79
ClinPred
0.89
D
GERP RS
6.0
Varity_R
0.32
gMVP
0.70

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: chr10-104356978; API