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GeneBe

10-16764458-A-T

Variant summary

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

The NM_012425.4(RSU1):c.213T>A(p.Phe71Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000263 in 152152 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

RSU1
NM_012425.4 missense

Scores

2
5
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.30

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSU1NM_012425.4 linkuse as main transcriptc.213T>A p.Phe71Leu missense_variant 4/9 ENST00000345264.10
RSU1NM_152724.3 linkuse as main transcriptc.54T>A p.Phe18Leu missense_variant 3/8
RSU1XM_047425617.1 linkuse as main transcriptc.213T>A p.Phe71Leu missense_variant 3/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSU1ENST00000345264.10 linkuse as main transcriptc.213T>A p.Phe71Leu missense_variant 4/91 NM_012425.4 P1Q15404-1

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152152
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000159
AC:
4
AN:
251298
Hom.:
0
AF XY:
0.0000147
AC XY:
2
AN XY:
135830
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000178
AC:
26
AN:
1461738
Hom.:
0
AF XY:
0.0000220
AC XY:
16
AN XY:
727172
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:
0.000104
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000144
Gnomad4 OTH exome
AF:
0.0000166
Bravo
AF:
0.0000227
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000165
AC:
2
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

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 GeneticsJun 24, 2022The c.213T>A (p.F71L) alteration is located in exon 4 (coding exon 3) of the RSU1 gene. This alteration results from a T to A substitution at nucleotide position 213, causing the phenylalanine (F) at amino acid position 71 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
1.0
BayesDel_addAF
Benign
-0.088
T
BayesDel_noAF
Benign
-0.13
Cadd
Uncertain
24
Dann
Uncertain
0.99
DEOGEN2
Benign
0.25
T;T;.
Eigen
Benign
0.16
Eigen_PC
Benign
0.12
FATHMM_MKL
Uncertain
0.83
D
M_CAP
Benign
0.042
D
MetaRNN
Uncertain
0.54
D;D;D
MetaSVM
Benign
-0.89
T
MutationAssessor
Benign
0.86
L;L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.90
D
PROVEAN
Uncertain
-3.5
D;D;.
REVEL
Uncertain
0.34
Sift
Benign
0.063
T;T;.
Sift4G
Benign
0.41
T;T;.
Polyphen
1.0
D;D;.
Vest4
0.79
MutPred
0.49
Gain of disorder (P = 0.1285);Gain of disorder (P = 0.1285);.;
MVP
0.60
MPC
0.36
ClinPred
0.57
D
GERP RS
0.70
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.30
gMVP
0.63

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: rs369457885; hg19: chr10-16806457; API