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GeneBe

1-152032745-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2_SupportingPP3_Strong

The NM_005620.2(S100A11):c.235G>A(p.Glu79Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

S100A11
NM_005620.2 missense

Scores

7
11
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.20

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PM1
?
In a binding_site (size 0) in uniprot entity S10AB_HUMAN
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.978

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
S100A11NM_005620.2 linkuse as main transcriptc.235G>A p.Glu79Lys missense_variant 3/3 ENST00000271638.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
S100A11ENST00000271638.3 linkuse as main transcriptc.235G>A p.Glu79Lys missense_variant 3/31 NM_005620.2 P1
ENST00000432386.1 linkuse as main transcriptn.2920-8840C>T intron_variant, non_coding_transcript_variant 2
S100A11ENST00000478109.1 linkuse as main transcriptn.318G>A non_coding_transcript_exon_variant 3/33

Frequencies

GnomAD3 genomes
Cov.:
33

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 GeneticsApr 22, 2022The c.235G>A (p.E79K) alteration is located in exon 3 (coding exon 3) of the S100A11 gene. This alteration results from a G to A substitution at nucleotide position 235, causing the glutamic acid (E) at amino acid position 79 to be replaced by a lysine (K). 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
0.95
BayesDel_addAF
Pathogenic
0.41
D
BayesDel_noAF
Pathogenic
0.35
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Pathogenic
0.92
D
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.87
D
M_CAP
Uncertain
0.091
D
MetaRNN
Pathogenic
0.98
D
MetaSVM
Uncertain
0.60
D
MutationAssessor
Pathogenic
3.6
H
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.72
T
PROVEAN
Uncertain
-3.7
D
REVEL
Pathogenic
0.78
Sift
Uncertain
0.025
D
Sift4G
Uncertain
0.027
D
Polyphen
0.28
B
Vest4
0.93
MutPred
0.89
Gain of methylation at E79 (P = 0.0088);
MVP
0.88
MPC
0.54
ClinPred
1.0
D
GERP RS
5.0
Varity_R
0.81
gMVP
0.88

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: rs1553188972; hg19: chr1-152005221; API