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GeneBe

12-45926500-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004719.3(SCAF11):c.3201G>T(p.Trp1067Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SCAF11
NM_004719.3 missense

Scores

4
11
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.22
Variant links:
Genes affected
SCAF11 (HGNC:10784): (SR-related CTD associated factor 11) Enables RNA binding activity. Involved in spliceosomal complex assembly. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCAF11NM_004719.3 linkuse as main transcriptc.3201G>T p.Trp1067Cys missense_variant 11/15 ENST00000369367.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCAF11ENST00000369367.8 linkuse as main transcriptc.3201G>T p.Trp1067Cys missense_variant 11/151 NM_004719.3 P1Q99590-1
SCAF11ENST00000549162.5 linkuse as main transcriptc.2625G>T p.Trp875Cys missense_variant 5/91
SCAF11ENST00000465950.5 linkuse as main transcriptc.2256G>T p.Trp752Cys missense_variant 1/51 Q99590-2
SCAF11ENST00000547950.1 linkuse as main transcriptn.211G>T non_coding_transcript_exon_variant 1/22

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 06, 2023The c.3201G>T (p.W1067C) alteration is located in exon 11 (coding exon 10) of the SCAF11 gene. This alteration results from a G to T substitution at nucleotide position 3201, causing the tryptophan (W) at amino acid position 1067 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.78
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.39
T;.;T
Eigen
Pathogenic
0.76
Eigen_PC
Pathogenic
0.75
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.95
D;D;D
M_CAP
Benign
0.046
D
MetaRNN
Uncertain
0.44
T;T;T
MetaSVM
Benign
-0.28
T
MutationAssessor
Uncertain
2.1
M;.;.
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Uncertain
0.54
T
PROVEAN
Uncertain
-4.4
D;D;D
REVEL
Uncertain
0.33
Sift
Uncertain
0.0010
D;D;D
Sift4G
Uncertain
0.011
D;D;D
Polyphen
1.0
D;.;D
Vest4
0.54
MutPred
0.32
Gain of catalytic residue at G1072 (P = 0.0155);.;.;
MVP
0.30
MPC
0.33
ClinPred
1.0
D
GERP RS
5.9
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.34
gMVP
0.24

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: chr12-46320283; API