chr9-104102043-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_006444.3(SMC2):c.720G>T(p.Leu240Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00050 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SMC2
NM_006444.3 missense
NM_006444.3 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 0.359
Genes affected
SMC2 (HGNC:14011): (structural maintenance of chromosomes 2) Predicted to enable ATP binding activity; chromatin binding activity; and single-stranded DNA binding activity. Involved in mitotic chromosome condensation. Located in condensed chromosome; cytoplasm; and nuclear lumen. Part of condensin complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.1854971).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC2 | NM_006444.3 | c.720G>T | p.Leu240Phe | missense_variant | 8/25 | ENST00000374793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC2 | ENST00000374793.8 | c.720G>T | p.Leu240Phe | missense_variant | 8/25 | 1 | NM_006444.3 | P1 | |
SMC2 | ENST00000286398.11 | c.720G>T | p.Leu240Phe | missense_variant | 8/25 | 1 | P1 | ||
SMC2 | ENST00000374787.7 | c.720G>T | p.Leu240Phe | missense_variant | 8/25 | 2 | P1 | ||
SMC2 | ENST00000440179.5 | c.285G>T | p.Leu95Phe | missense_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151024Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000499 AC: 686AN: 1375840Hom.: 0 Cov.: 31 AF XY: 0.000452 AC XY: 310AN XY: 686550
GnomAD4 exome
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 151150Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73872
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.720G>T (p.L240F) alteration is located in exon 8 (coding exon 7) of the SMC2 gene. This alteration results from a G to T substitution at nucleotide position 720, causing the leucine (L) at amino acid position 240 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;.;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N;N
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;.;B;B
Vest4
MutPred
Loss of disorder (P = 0.1976);.;Loss of disorder (P = 0.1976);Loss of disorder (P = 0.1976);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.