Menu
GeneBe

10-16752625-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_012425.4(RSU1):c.512C>T(p.Ser171Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000040 ( 0 hom. )

Consequence

RSU1
NM_012425.4 missense

Scores

1
4
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.71

Links

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSU1NM_012425.4 linkuse as main transcriptc.512C>T p.Ser171Leu missense_variant 7/9 ENST00000345264.10
RSU1NM_152724.3 linkuse as main transcriptc.353C>T p.Ser118Leu missense_variant 6/8
RSU1XM_047425617.1 linkuse as main transcriptc.512C>T p.Ser171Leu missense_variant 6/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSU1ENST00000345264.10 linkuse as main transcriptc.512C>T p.Ser171Leu missense_variant 7/91 NM_012425.4 P1Q15404-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251372
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135852
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
AF:
0.00000479
AC:
7
AN:
1461750
Hom.:
0
AF XY:
0.00000275
AC XY:
2
AN XY:
727194
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000360
Gnomad4 OTH exome
AF:
0.0000166
Bravo
AF:
0.00000378
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 06, 2021The c.512C>T (p.S171L) alteration is located in exon 7 (coding exon 6) of the RSU1 gene. This alteration results from a C to T substitution at nucleotide position 512, causing the serine (S) at amino acid position 171 to be replaced by a leucine (L). 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
0.12
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.35
Cadd
Benign
22
Dann
Uncertain
0.99
DEOGEN2
Benign
0.18
T;T;.
Eigen
Benign
0.060
Eigen_PC
Benign
0.14
FATHMM_MKL
Pathogenic
0.98
D
M_CAP
Benign
0.037
D
MetaRNN
Uncertain
0.53
D;D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.3
L;L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.78
T
PROVEAN
Uncertain
-4.0
D;D;.
REVEL
Benign
0.24
Sift
Benign
0.049
D;D;.
Sift4G
Benign
0.24
T;T;.
Polyphen
0.92
P;P;.
Vest4
0.67
MutPred
0.35
Loss of disorder (P = 0.052);Loss of disorder (P = 0.052);.;
MVP
0.23
MPC
0.27
ClinPred
0.57
D
GERP RS
4.3
Varity_R
0.13
gMVP
0.70

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs759133204; hg19: chr10-16794624; COSMIC: COSV105252963; COSMIC: COSV105252963; API