rs6709886
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001164507.2(NEB):c.9363T>G(p.Pro3121=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,776 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. P3121P) has been classified as Benign.
Frequency
Consequence
NM_001164507.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.9363T>G | p.Pro3121= | synonymous_variant | 65/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.9363T>G | p.Pro3121= | synonymous_variant | 65/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.9363T>G | p.Pro3121= | synonymous_variant | 65/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.9363T>G | p.Pro3121= | synonymous_variant | 65/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.8854-2527T>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249022Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135084
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461664Hom.: 0 Cov.: 102 AF XY: 0.0000289 AC XY: 21AN XY: 727100
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Counsyl | May 19, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at