rs747466015
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001164507.2(NEB):āc.8690T>Cā(p.Met2897Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.8690T>C | p.Met2897Thr | missense_variant | 62/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.8690T>C | p.Met2897Thr | missense_variant | 62/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.8690T>C | p.Met2897Thr | missense_variant | 62/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.8690T>C | p.Met2897Thr | missense_variant | 62/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.8690T>C | p.Met2897Thr | missense_variant | 62/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248860Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135006
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460402Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726532
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74366
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 26, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at