chr6-27309131-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_033482.4(POM121L2):c.3040G>A(p.Ala1014Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,551,720 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
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.3040G>A | p.Ala1014Thr | missense_variant | 1/1 | ENST00000444565.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POM121L2 | ENST00000444565.2 | c.3040G>A | p.Ala1014Thr | missense_variant | 1/1 | NM_033482.4 | P1 | ||
POM121L2 | ENST00000429945.1 | c.216+1966G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 5AN: 157106Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83168
GnomAD4 exome AF: 0.0000279 AC: 39AN: 1399472Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 19AN XY: 690242
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | 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