rs369953387

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001129993.3(SANBR):​c.494C>A​(p.Pro165Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. P165L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

SANBR
NM_001129993.3 missense

Scores

8
7
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.87
Variant links:
Genes affected
SANBR (HGNC:29387): (SANT and BTB domain regulator of CSR)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.767

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SANBRNM_001129993.3 linkc.494C>A p.Pro165Gln missense_variant Exon 6 of 22 ENST00000402291.6 NP_001123465.1 Q6NSI8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SANBRENST00000402291.6 linkc.494C>A p.Pro165Gln missense_variant Exon 6 of 22 1 NM_001129993.3 ENSP00000385579.1 Q6NSI8-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461812
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
727196
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.43
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Pathogenic
0.14
CADD
Pathogenic
28
DANN
Uncertain
0.99
DEOGEN2
Benign
0.28
T;.;T;.;.
Eigen
Pathogenic
0.88
Eigen_PC
Pathogenic
0.87
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.95
.;.;D;D;D
M_CAP
Benign
0.029
D
MetaRNN
Pathogenic
0.77
D;D;D;D;D
MetaSVM
Benign
-0.91
T
MutationAssessor
Uncertain
2.9
M;M;M;.;M
PrimateAI
Pathogenic
0.81
D
PROVEAN
Pathogenic
-6.1
D;D;D;.;D
REVEL
Uncertain
0.64
Sift
Uncertain
0.0030
D;D;D;.;D
Sift4G
Uncertain
0.011
D;D;D;T;D
Polyphen
1.0
D;D;D;.;D
Vest4
0.68
MutPred
0.63
Gain of solvent accessibility (P = 0.0374);Gain of solvent accessibility (P = 0.0374);Gain of solvent accessibility (P = 0.0374);.;Gain of solvent accessibility (P = 0.0374);
MVP
0.72
MPC
0.42
ClinPred
0.99
D
GERP RS
5.7
Varity_R
0.67
gMVP
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: chr2-61304117; API