chr4-153583586-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001131007.2(TMEM131L):c.974G>C(p.Arg325Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,610,934 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 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.974G>C | p.Arg325Thr | missense_variant | 11/35 | ENST00000409959.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM131L | ENST00000409959.8 | c.974G>C | p.Arg325Thr | missense_variant | 11/35 | 5 | NM_001131007.2 | A2 | |
TMEM131L | ENST00000240487.5 | c.557G>C | p.Arg186Thr | missense_variant | 7/29 | 1 | |||
TMEM131L | ENST00000409663.7 | c.974G>C | p.Arg325Thr | missense_variant | 11/35 | 5 | P4 | ||
TMEM131L | ENST00000509565.1 | n.49G>C | non_coding_transcript_exon_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249214Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134596
GnomAD4 exome AF: 0.000123 AC: 180AN: 1458738Hom.: 0 Cov.: 29 AF XY: 0.000130 AC XY: 94AN XY: 725712
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2023 | The c.974G>C (p.R325T) alteration is located in exon 11 (coding exon 11) of the KIAA0922 gene. This alteration results from a G to C substitution at nucleotide position 974, causing the arginine (R) at amino acid position 325 to be replaced by a threonine (T). 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