chr9-104102499-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006444.3(SMC2):c.946G>A(p.Ala316Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A316S) has been classified as Uncertain significance.
Frequency
Consequence
NM_006444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC2 | NM_006444.3 | c.946G>A | p.Ala316Thr | missense_variant | 9/25 | ENST00000374793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC2 | ENST00000374793.8 | c.946G>A | p.Ala316Thr | missense_variant | 9/25 | 1 | NM_006444.3 | P1 | |
SMC2 | ENST00000286398.11 | c.946G>A | p.Ala316Thr | missense_variant | 9/25 | 1 | P1 | ||
SMC2 | ENST00000374787.7 | c.946G>A | p.Ala316Thr | missense_variant | 9/25 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152080Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250786Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135558
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461332Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726970
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.946G>A (p.A316T) alteration is located in exon 9 (coding exon 8) of the SMC2 gene. This alteration results from a G to A substitution at nucleotide position 946, causing the alanine (A) at amino acid position 316 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at