2-151655904-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001164507.2(NEB):c.6615C>T(p.Arg2205=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,613,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R2205R) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.6615C>T | p.Arg2205= | synonymous_variant | 50/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.6615C>T | p.Arg2205= | synonymous_variant | 50/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.6615C>T | p.Arg2205= | synonymous_variant | 50/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.6615C>T | p.Arg2205= | synonymous_variant | 50/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.6615C>T | p.Arg2205= | synonymous_variant | 50/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249056Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135108
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461554Hom.: 0 Cov.: 32 AF XY: 0.0000743 AC XY: 54AN XY: 727068
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at