NM_001348680.2:c.688G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001348680.2(SAP25):​c.688G>T​(p.Gly230Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 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. G230S) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

SAP25
NM_001348680.2 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.952

Publications

0 publications found
Variant links:
Genes affected
SAP25 (HGNC:41908): (Sin3A associated protein 25) Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19203386).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SAP25NM_001348680.2 linkc.688G>T p.Gly230Cys missense_variant Exon 6 of 6 ENST00000622764.3 NP_001335609.1
SAP25NM_001168682.3 linkc.667G>T p.Gly223Cys missense_variant Exon 6 of 6 NP_001162153.2
SAP25NM_001348677.2 linkc.394G>T p.Gly132Cys missense_variant Exon 5 of 5 NP_001335606.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SAP25ENST00000622764.3 linkc.688G>T p.Gly230Cys missense_variant Exon 6 of 6 5 NM_001348680.2 ENSP00000481773.2 A0A087WYF9

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.48
CADD
Benign
15
DANN
Uncertain
0.99
DEOGEN2
Benign
0.039
T;.;T
Eigen
Benign
-0.55
Eigen_PC
Benign
-0.73
FATHMM_MKL
Benign
0.059
N
LIST_S2
Benign
0.39
.;T;T
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.19
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.5
L;.;L
PhyloP100
-0.95
PrimateAI
Benign
0.42
T
PROVEAN
Uncertain
-2.4
N;.;.
REVEL
Benign
0.057
Sift
Uncertain
0.012
D;.;.
Sift4G
Benign
0.062
T;T;T
Polyphen
1.0
D;.;D
Vest4
0.29
MutPred
0.15
Loss of methylation at R131 (P = 0.0537);.;Loss of methylation at R131 (P = 0.0537);
MVP
0.076
ClinPred
0.30
T
GERP RS
2.3
Varity_R
0.15
gMVP
0.097
Mutation Taster
=98/2
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs540582443; hg19: chr7-100170116; API