6-27309287-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_033482.4(POM121L2):c.2884G>A(p.Ala962Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000277 in 1,551,322 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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. A962V) has been classified as Uncertain significance.
Frequency
Consequence
NM_033482.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POM121L2 | NM_033482.4 | c.2884G>A | p.Ala962Thr | missense_variant | 1/1 | ENST00000444565.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POM121L2 | ENST00000444565.2 | c.2884G>A | p.Ala962Thr | missense_variant | 1/1 | NM_033482.4 | P1 | ||
POM121L2 | ENST00000429945.1 | c.216+1810G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000255 AC: 4AN: 156756Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82892
GnomAD4 exome AF: 0.0000286 AC: 40AN: 1399132Hom.: 2 Cov.: 31 AF XY: 0.0000188 AC XY: 13AN XY: 690010
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.2884G>A (p.A962T) alteration is located in exon 1 (coding exon 1) of the POM121L2 gene. This alteration results from a G to A substitution at nucleotide position 2884, causing the alanine (A) at amino acid position 962 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