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GeneBe

10-16817018-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PM2_SupportingBP4

The NM_012425.4(RSU1):c.64A>G(p.Met22Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

RSU1
NM_012425.4 missense

Scores

3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.34

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3657141).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSU1NM_012425.4 linkuse as main transcriptc.64A>G p.Met22Val missense_variant 2/9 ENST00000345264.10
RSU1XM_047425617.1 linkuse as main transcriptc.64A>G p.Met22Val missense_variant 1/7
RSU1NM_152724.3 linkuse as main transcriptc.-51+297A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSU1ENST00000345264.10 linkuse as main transcriptc.64A>G p.Met22Val missense_variant 2/91 NM_012425.4 P1Q15404-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461868
Hom.:
0
AF XY:
0.00000275
AC XY:
2
AN XY:
727242
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:
0.00000180
Gnomad4 OTH exome
AF:
0.00
Bravo
AF:
0.00000378

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 19, 2022The c.64A>G (p.M22V) alteration is located in exon 2 (coding exon 1) of the RSU1 gene. This alteration results from a A to G substitution at nucleotide position 64, causing the methionine (M) at amino acid position 22 to be replaced by a valine (V). 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
0.20
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
Cadd
Uncertain
24
Dann
Uncertain
0.99
DEOGEN2
Benign
0.026
T;T
Eigen
Benign
-0.19
Eigen_PC
Benign
-0.0051
FATHMM_MKL
Benign
0.31
N
M_CAP
Benign
0.022
T
MetaRNN
Benign
0.37
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.1
L;L
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-0.91
N;N
REVEL
Benign
0.074
Sift
Benign
0.032
D;D
Sift4G
Uncertain
0.036
D;D
Polyphen
0.0010
B;B
Vest4
0.65
MutPred
0.54
Loss of catalytic residue at M22 (P = 0.0595);Loss of catalytic residue at M22 (P = 0.0595);
MVP
0.40
MPC
0.30
ClinPred
0.45
T
GERP RS
4.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.41
gMVP
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.34
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.34
Position offset: 1

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: rs1588555975; hg19: chr10-16859017; API