chr12-89421264-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_172240.3(POC1B):c.1333-7T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,424,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_172240.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POC1B | NM_172240.3 | c.1333-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000313546.8 | |||
LOC124902981 | XR_007063401.1 | n.527-3442A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POC1B | ENST00000313546.8 | c.1333-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_172240.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000853 AC: 2AN: 234418Hom.: 0 AF XY: 0.00000792 AC XY: 1AN XY: 126300
GnomAD4 exome AF: 0.0000119 AC: 17AN: 1424778Hom.: 0 Cov.: 28 AF XY: 0.00000710 AC XY: 5AN XY: 704130
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at