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GeneBe

1-152032768-C-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_005620.2(S100A11):c.212G>C(p.Ser71Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign 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

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.525

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.1911861).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
S100A11NM_005620.2 linkuse as main transcriptc.212G>C p.Ser71Thr missense_variant 3/3 ENST00000271638.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
S100A11ENST00000271638.3 linkuse as main transcriptc.212G>C p.Ser71Thr missense_variant 3/31 NM_005620.2 P1
ENST00000432386.1 linkuse as main transcriptn.2920-8817C>G intron_variant, non_coding_transcript_variant 2
S100A11ENST00000478109.1 linkuse as main transcriptn.295G>C 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 GeneticsMay 05, 2022The c.212G>C (p.S71T) alteration is located in exon 3 (coding exon 3) of the S100A11 gene. This alteration results from a G to C substitution at nucleotide position 212, causing the serine (S) at amino acid position 71 to be replaced by a threonine (T). 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
0.13
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.55
Cadd
Benign
3.0
Dann
Benign
0.67
DEOGEN2
Benign
0.42
T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.038
N
LIST_S2
Benign
0.79
T
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.19
T
MetaSVM
Benign
-0.83
T
MutationAssessor
Uncertain
2.5
M
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-1.6
N
REVEL
Benign
0.21
Sift
Benign
0.27
T
Sift4G
Benign
0.44
T
Polyphen
0.078
B
Vest4
0.11
MutPred
0.32
Loss of disorder (P = 0.0964);
MVP
0.29
MPC
0.23
ClinPred
0.42
T
GERP RS
-4.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.084
gMVP
0.15

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-152005244; API