chr12-56164654-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001330288.2(SMARCC2):c.3310G>A(p.Val1104Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000672 in 1,612,444 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330288.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCC2 | NM_001330288.2 | c.3310G>A | p.Val1104Met | missense_variant | 28/29 | ENST00000550164.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCC2 | ENST00000550164.6 | c.3310G>A | p.Val1104Met | missense_variant | 28/29 | 5 | NM_001330288.2 | A2 | |
ENST00000553176.1 | n.213-2105G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000499 AC: 76AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000503 AC: 124AN: 246356Hom.: 0 AF XY: 0.000510 AC XY: 68AN XY: 133304
GnomAD4 exome AF: 0.000690 AC: 1008AN: 1460152Hom.: 2 Cov.: 32 AF XY: 0.000661 AC XY: 480AN XY: 726302
GnomAD4 genome ? AF: 0.000499 AC: 76AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74472
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.3217G>A (p.V1073M) alteration is located in exon 27 (coding exon 27) of the SMARCC2 gene. This alteration results from a G to A substitution at nucleotide position 3217, causing the valine (V) at amino acid position 1073 to be replaced by a methionine (M). 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