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GeneBe

12-45924924-G-C

Variant summary

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

The NM_004719.3(SCAF11):c.3710C>G(p.Ala1237Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SCAF11
NM_004719.3 missense

Scores

2
4
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.51
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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2628417).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCAF11NM_004719.3 linkuse as main transcriptc.3710C>G p.Ala1237Gly missense_variant 12/15 ENST00000369367.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCAF11ENST00000369367.8 linkuse as main transcriptc.3710C>G p.Ala1237Gly missense_variant 12/151 NM_004719.3 P1Q99590-1
SCAF11ENST00000549162.5 linkuse as main transcriptc.3134C>G p.Ala1045Gly missense_variant 6/91
SCAF11ENST00000465950.5 linkuse as main transcriptc.2765C>G p.Ala922Gly missense_variant 2/51 Q99590-2
SCAF11ENST00000547950.1 linkuse as main transcript downstream_gene_variant 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000400
AC:
1
AN:
250020
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135300
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
34
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 GeneticsJan 30, 2024The c.3710C>G (p.A1237G) alteration is located in exon 12 (coding exon 11) of the SCAF11 gene. This alteration results from a C to G substitution at nucleotide position 3710, causing the alanine (A) at amino acid position 1237 to be replaced by a glycine (G). 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
Benign
0.24
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.41
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.019
T;.;T
Eigen
Uncertain
0.66
Eigen_PC
Pathogenic
0.66
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.89
D;D;D
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.26
T;T;T
MetaSVM
Benign
-0.80
T
MutationAssessor
Benign
1.8
L;.;.
MutationTaster
Benign
0.98
N;N;N;N
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-0.98
N;N;N
REVEL
Benign
0.15
Sift
Uncertain
0.028
D;D;D
Sift4G
Benign
0.16
T;T;T
Polyphen
0.99
D;.;.
Vest4
0.25
MutPred
0.35
Gain of catalytic residue at A1237 (P = 0);.;.;
MVP
0.32
MPC
0.26
ClinPred
0.74
D
GERP RS
5.1
Varity_R
0.12
gMVP
0.25

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: rs752583297; hg19: chr12-46318707; API