chr12-6837958-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_014262.5(P3H3):c.1830C>T(p.Ser610=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000785 in 1,604,712 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014262.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P3H3 | NM_014262.5 | c.1830C>T | p.Ser610= | splice_region_variant, synonymous_variant | 13/15 | ENST00000290510.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P3H3 | ENST00000290510.10 | c.1830C>T | p.Ser610= | splice_region_variant, synonymous_variant | 13/15 | 1 | NM_014262.5 | P1 | |
P3H3 | ENST00000612048.4 | n.1363C>T | splice_region_variant, non_coding_transcript_exon_variant | 12/14 | 1 | ||||
P3H3 | ENST00000536140.5 | n.2460C>T | splice_region_variant, non_coding_transcript_exon_variant | 14/16 | 2 | ||||
P3H3 | ENST00000544200.5 | n.869C>T | splice_region_variant, non_coding_transcript_exon_variant | 8/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000103 AC: 24AN: 233630Hom.: 0 AF XY: 0.0000870 AC XY: 11AN XY: 126494
GnomAD4 exome AF: 0.0000757 AC: 110AN: 1452470Hom.: 1 Cov.: 33 AF XY: 0.0000832 AC XY: 60AN XY: 721570
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | P3H3: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at