chr4-153466414-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001131007.2(TMEM131L):c.17G>A(p.Arg6His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000303 in 1,351,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R6L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001131007.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM131L | NM_001131007.2 | c.17G>A | p.Arg6His | missense_variant | 1/35 | ENST00000409959.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM131L | ENST00000409959.8 | c.17G>A | p.Arg6His | missense_variant | 1/35 | 5 | NM_001131007.2 | A2 | |
TMEM131L | ENST00000409663.7 | c.17G>A | p.Arg6His | missense_variant | 1/35 | 5 | P4 | ||
TMEM131L | ENST00000445960.5 | c.17G>A | p.Arg6His | missense_variant, NMD_transcript_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151262Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000317 AC: 38AN: 1200328Hom.: 0 Cov.: 29 AF XY: 0.0000324 AC XY: 19AN XY: 586622
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151262Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73826
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2023 | The c.17G>A (p.R6H) alteration is located in exon 1 (coding exon 1) of the KIAA0922 gene. This alteration results from a G to A substitution at nucleotide position 17, causing the arginine (R) at amino acid position 6 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at