6-27309370-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_033482.4(POM121L2):c.2801C>T(p.Pro934Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,551,590 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POM121L2 | NM_033482.4 | c.2801C>T | p.Pro934Leu | missense_variant | 1/1 | ENST00000444565.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POM121L2 | ENST00000444565.2 | c.2801C>T | p.Pro934Leu | missense_variant | 1/1 | NM_033482.4 | P1 | ||
POM121L2 | ENST00000429945.1 | c.216+1727C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000703 AC: 107AN: 152174Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000550 AC: 86AN: 156412Hom.: 0 AF XY: 0.000543 AC XY: 45AN XY: 82888
GnomAD4 exome AF: 0.00135 AC: 1884AN: 1399298Hom.: 1 Cov.: 31 AF XY: 0.00126 AC XY: 870AN XY: 690162
GnomAD4 genome ? AF: 0.000703 AC: 107AN: 152292Hom.: 1 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | POM121L2: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at