1-46673056-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001145474.4(TEX38):c.221G>A(p.Arg74His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,551,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001145474.4 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 |
---|---|---|---|---|---|---|---|---|
TEX38 | NM_001145474.4 | c.221G>A | p.Arg74His | missense_variant | 2/2 | ENST00000334122.5 | NP_001138946.1 | |
TEX38 | NM_001300863.2 | c.59G>A | p.Arg20His | missense_variant | 2/2 | NP_001287792.1 | ||
TEX38 | XM_011541421.4 | c.224G>A | p.Arg75His | missense_variant | 2/2 | XP_011539723.1 | ||
TEX38 | NM_001300864.2 | c.-8G>A | 5_prime_UTR_variant | 2/2 | NP_001287793.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 18AN: 156300Hom.: 0 AF XY: 0.000133 AC XY: 11AN XY: 82834
GnomAD4 exome AF: 0.0000307 AC: 43AN: 1399424Hom.: 0 Cov.: 31 AF XY: 0.0000319 AC XY: 22AN XY: 690216
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 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