1-151847780-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_182578.4(THEM5):c.658G>A(p.Ala220Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,613,788 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 (★).
Frequency
Consequence
NM_182578.4 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 | UniProt |
---|---|---|---|---|---|---|---|
THEM5 | NM_182578.4 | c.658G>A | p.Ala220Thr | missense_variant | 5/6 | ENST00000368817.10 | |
C2CD4D-AS1 | NR_024237.2 | n.1031-2453C>T | intron_variant, non_coding_transcript_variant | ||||
THEM5 | XM_011509421.2 | c.576-366G>A | intron_variant | ||||
C2CD4D-AS1 | NR_152846.1 | n.951-2453C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THEM5 | ENST00000368817.10 | c.658G>A | p.Ala220Thr | missense_variant | 5/6 | 1 | NM_182578.4 | P1 | |
C2CD4D-AS1 | ENST00000434182.1 | n.354-2453C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
THEM5 | ENST00000453881.2 | c.223-366G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 151966Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251450Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135902
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461822Hom.: 0 Cov.: 34 AF XY: 0.0000646 AC XY: 47AN XY: 727200
GnomAD4 genome AF: 0.0000855 AC: 13AN: 151966Hom.: 0 Cov.: 30 AF XY: 0.0000943 AC XY: 7AN XY: 74218
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2023 | 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