chr6-27309073-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033482.4(POM121L2):c.3098A>G(p.Tyr1033Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,549,240 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033482.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POM121L2 | NM_033482.4 | c.3098A>G | p.Tyr1033Cys | missense_variant | 1/1 | ENST00000444565.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POM121L2 | ENST00000444565.2 | c.3098A>G | p.Tyr1033Cys | missense_variant | 1/1 | NM_033482.4 | P1 | ||
POM121L2 | ENST00000429945.1 | c.216+2024A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000770 AC: 12AN: 155916Hom.: 0 AF XY: 0.0000365 AC XY: 3AN XY: 82266
GnomAD4 exome AF: 0.0000222 AC: 31AN: 1396892Hom.: 1 Cov.: 30 AF XY: 0.0000189 AC XY: 13AN XY: 688790
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.3098A>G (p.Y1033C) alteration is located in exon 1 (coding exon 1) of the POM121L2 gene. This alteration results from a A to G substitution at nucleotide position 3098, causing the tyrosine (Y) at amino acid position 1033 to be replaced by a cysteine (C). 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