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GeneBe

10-16754881-G-T

Variant summary

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

The NM_012425.4(RSU1):c.390C>A(p.Phe130Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000197 in 152204 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 31)

Consequence

RSU1
NM_012425.4 missense

Scores

4
8
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.18

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, gnomad allele frequency = 0.0000197 (3/152204) while in subpopulation AFR AF= 0.0000724 (3/41450). AF 95% confidence interval is 0.0000192. There are 0 homozygotes in gnomad. There are 3 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSU1NM_012425.4 linkuse as main transcriptc.390C>A p.Phe130Leu missense_variant 5/9 ENST00000345264.10
RSU1NM_152724.3 linkuse as main transcriptc.231C>A p.Phe77Leu missense_variant 4/8
RSU1XM_047425617.1 linkuse as main transcriptc.390C>A p.Phe130Leu missense_variant 4/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSU1ENST00000345264.10 linkuse as main transcriptc.390C>A p.Phe130Leu missense_variant 5/91 NM_012425.4 P1Q15404-1

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152204
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
Bravo
AF:
0.0000151

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 GeneticsAug 13, 2021The c.390C>A (p.F130L) alteration is located in exon 5 (coding exon 4) of the RSU1 gene. This alteration results from a C to A substitution at nucleotide position 390, causing the phenylalanine (F) at amino acid position 130 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
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.20
D
BayesDel_noAF
Uncertain
0.040
Cadd
Pathogenic
28
Dann
Uncertain
1.0
DEOGEN2
Benign
0.27
T;T;.
Eigen
Uncertain
0.24
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Uncertain
0.97
D
M_CAP
Benign
0.024
T
MetaRNN
Uncertain
0.74
D;D;D
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.45
N;N;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.86
D
PROVEAN
Pathogenic
-5.1
D;D;.
REVEL
Uncertain
0.36
Sift
Uncertain
0.011
D;D;.
Sift4G
Benign
0.16
T;T;.
Polyphen
0.98
D;D;.
Vest4
0.76
MutPred
0.54
Loss of catalytic residue at F130 (P = 0.0557);Loss of catalytic residue at F130 (P = 0.0557);.;
MVP
0.58
MPC
0.39
ClinPred
0.99
D
GERP RS
4.3
Varity_R
0.72
gMVP
0.73

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: rs1303596198; hg19: chr10-16796880; API