chr1-37822664-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005955.3(MTF1):c.1224G>A(p.Pro408=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,613,452 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000079 ( 2 hom. )
Consequence
MTF1
NM_005955.3 synonymous
NM_005955.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.275
Genes affected
MTF1 (HGNC:7428): (metal regulatory transcription factor 1) This gene encodes a transcription factor that induces expression of metallothioneins and other genes involved in metal homeostasis in response to heavy metals such as cadmium, zinc, copper, and silver. The protein is a nucleocytoplasmic shuttling protein that accumulates in the nucleus upon heavy metal exposure and binds to promoters containing a metal-responsive element (MRE). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 1-37822664-C-T is Benign according to our data. Variant chr1-37822664-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 730186.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.275 with no splicing effect.
BS2
?
High AC in GnomAd at 32 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTF1 | NM_005955.3 | c.1224G>A | p.Pro408= | synonymous_variant | 9/11 | ENST00000373036.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTF1 | ENST00000373036.5 | c.1224G>A | p.Pro408= | synonymous_variant | 9/11 | 1 | NM_005955.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000211 AC: 32AN: 151964Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000112 AC: 28AN: 249834Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135114
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GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461370Hom.: 2 Cov.: 31 AF XY: 0.0000702 AC XY: 51AN XY: 726934
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GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74336
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at