chr1-37823790-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_005955.3(MTF1):c.1091C>T(p.Thr364Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00482 in 1,613,962 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0028 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0050 ( 27 hom. )
Consequence
MTF1
NM_005955.3 missense
NM_005955.3 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 4.10
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 -9 ACMG points.
PP2
Missense variant where missense usually causes diseases, MTF1
BP4
Computational evidence support a benign effect (MetaRNN=0.004799485).
BP6
Variant 1-37823790-G-A is Benign according to our data. Variant chr1-37823790-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 715469.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 420 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTF1 | NM_005955.3 | c.1091C>T | p.Thr364Ile | missense_variant | 8/11 | ENST00000373036.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTF1 | ENST00000373036.5 | c.1091C>T | p.Thr364Ile | missense_variant | 8/11 | 1 | NM_005955.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00276 AC: 420AN: 152178Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00251 AC: 630AN: 251398Hom.: 2 AF XY: 0.00253 AC XY: 344AN XY: 135870
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GnomAD4 exome AF: 0.00503 AC: 7356AN: 1461666Hom.: 27 Cov.: 31 AF XY: 0.00499 AC XY: 3626AN XY: 727142
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GnomAD4 genome AF: 0.00276 AC: 420AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00262 AC XY: 195AN XY: 74480
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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 | Oct 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at