22-37069345-CTGGGGTGGGGTGGGGTGGGG-CTGGGGTGGGGTGGGGTGGGGTGGGGTGGGGTGGGGTGGGG
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 4P and 5B. PVS1_StrongBP6BS1
The NM_001374504.1(TMPRSS6):c.1842-21_1842-2dupCCCCACCCCACCCCACCCCA variant causes a splice acceptor, intron change. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001374504.1 splice_acceptor, intron
Scores
Clinical Significance
Conservation
Publications
- IRIDA syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, Genomics England PanelApp
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMPRSS6 | NM_001374504.1 | c.1842-21_1842-2dupCCCCACCCCACCCCACCCCA | splice_acceptor_variant, intron_variant | Intron 15 of 17 | ENST00000676104.1 | NP_001361433.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000242 AC: 22AN: 90956Hom.: 0 Cov.: 0 show subpopulations
GnomAD4 exome AF: 0.0000427 AC: 14AN: 327526Hom.: 0 Cov.: 0 AF XY: 0.0000294 AC XY: 5AN XY: 170130 show subpopulations
GnomAD4 genome AF: 0.000264 AC: 24AN: 91028Hom.: 1 Cov.: 0 AF XY: 0.000255 AC XY: 11AN XY: 43058 show subpopulations
ClinVar
Submissions by phenotype
TMPRSS6-related disorder Benign:1
This variant is classified as likely 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