14-58138232-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001001872.4(ARMH4):c.1127C>T(p.Thr376Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000762 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001001872.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMH4 | NM_001001872.4 | c.1127C>T | p.Thr376Met | missense_variant | 2/8 | ENST00000267485.7 | NP_001001872.2 | |
ARMH4 | NM_001320173.3 | c.1127C>T | p.Thr376Met | missense_variant | 2/5 | NP_001307102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMH4 | ENST00000267485.7 | c.1127C>T | p.Thr376Met | missense_variant | 2/8 | 1 | NM_001001872.4 | ENSP00000267485 | P1 | |
ARMH4 | ENST00000334342.5 | n.1292C>T | non_coding_transcript_exon_variant | 2/5 | 1 | |||||
ARMH4 | ENST00000557175.5 | n.894+116C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251406Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135878
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461784Hom.: 0 Cov.: 32 AF XY: 0.0000880 AC XY: 64AN XY: 727204
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at