7-39433070-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BA1
The NM_001370959.1(POU6F2):c.1114-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,612,578 control chromosomes in the GnomAD database, including 58,903 homozygotes. 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 Benign (no stars).
Frequency
Consequence
NM_001370959.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POU6F2 | NM_001370959.1 | c.1114-7C>T | splice_region_variant, intron_variant | Intron 6 of 9 | ENST00000518318.7 | NP_001357888.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POU6F2 | ENST00000518318.7 | c.1114-7C>T | splice_region_variant, intron_variant | Intron 6 of 9 | 1 | NM_001370959.1 | ENSP00000430514.3 |
Frequencies
GnomAD3 genomes AF: 0.288 AC: 43596AN: 151598Hom.: 6625 Cov.: 31
GnomAD3 exomes AF: 0.284 AC: 70791AN: 249264Hom.: 10664 AF XY: 0.277 AC XY: 37292AN XY: 134818
GnomAD4 exome AF: 0.263 AC: 384374AN: 1460862Hom.: 52268 Cov.: 34 AF XY: 0.261 AC XY: 189473AN XY: 726724
GnomAD4 genome AF: 0.288 AC: 43637AN: 151716Hom.: 6635 Cov.: 31 AF XY: 0.289 AC XY: 21394AN XY: 74116
ClinVar
Submissions by phenotype
POU6F2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at