22-37066133-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001374504.1(TMPRSS6):c.2356G>A(p.Val786Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0101 in 1,613,366 control chromosomes in the GnomAD database, including 100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001374504.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMPRSS6 | NM_001374504.1 | c.2356G>A | p.Val786Ile | missense_variant | Exon 18 of 18 | ENST00000676104.1 | NP_001361433.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00830 AC: 1263AN: 152104Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00805 AC: 2008AN: 249464Hom.: 16 AF XY: 0.00799 AC XY: 1081AN XY: 135254
GnomAD4 exome AF: 0.0103 AC: 15005AN: 1461144Hom.: 96 Cov.: 32 AF XY: 0.00982 AC XY: 7138AN XY: 726864
GnomAD4 genome AF: 0.00829 AC: 1262AN: 152222Hom.: 4 Cov.: 33 AF XY: 0.00842 AC XY: 627AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
See Variant Classification Assertion Criteria. -
- -
BS1, BS2 -
TMPRSS6: BS1, BS2 -
not specified Benign:1
- -
Microcytic anemia Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at