chr9-104098498-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006444.3(SMC2):c.371A>C(p.Asn124Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00679 in 1,598,840 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0044 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0070 ( 46 hom. )
Consequence
SMC2
NM_006444.3 missense
NM_006444.3 missense
Scores
8
11
Clinical Significance
Conservation
PhyloP100: 5.05
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 Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.00913018).
BP6
?
Variant 9-104098498-A-C is Benign according to our data. Variant chr9-104098498-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 787626.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 670 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC2 | NM_006444.3 | c.371A>C | p.Asn124Thr | missense_variant | 4/25 | ENST00000374793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC2 | ENST00000374793.8 | c.371A>C | p.Asn124Thr | missense_variant | 4/25 | 1 | NM_006444.3 | P1 | |
SMC2 | ENST00000286398.11 | c.371A>C | p.Asn124Thr | missense_variant | 4/25 | 1 | P1 | ||
SMC2 | ENST00000374787.7 | c.371A>C | p.Asn124Thr | missense_variant | 4/25 | 2 | P1 | ||
SMC2 | ENST00000440179.5 | c.-65A>C | 5_prime_UTR_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00440 AC: 670AN: 152170Hom.: 2 Cov.: 33
GnomAD3 genomes
?
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670
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152170
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33
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GnomAD3 exomes AF: 0.00413 AC: 979AN: 236794Hom.: 2 AF XY: 0.00428 AC XY: 549AN XY: 128250
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GnomAD4 exome AF: 0.00704 AC: 10186AN: 1446552Hom.: 46 Cov.: 28 AF XY: 0.00689 AC XY: 4958AN XY: 719436
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GnomAD4 genome ? AF: 0.00440 AC: 670AN: 152288Hom.: 2 Cov.: 33 AF XY: 0.00411 AC XY: 306AN XY: 74472
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ESP6500AA
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6
ESP6500EA
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68
ExAC
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530
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at