rs1316893006
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004006.3(DMD):āc.6704G>Cā(p.Ser2235Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000241 in 1,203,335 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S2235N) has been classified as Likely benign.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.6704G>C | p.Ser2235Thr | missense_variant | 46/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.6704G>C | p.Ser2235Thr | missense_variant | 46/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111835Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34011
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183053Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67647
GnomAD4 exome AF: 0.0000247 AC: 27AN: 1091500Hom.: 0 Cov.: 29 AF XY: 0.0000196 AC XY: 7AN XY: 357140
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111835Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34011
ClinVar
Submissions by phenotype
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at