chr7-100620863-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003227.4(TFR2):c.2400C>T(p.Asn800=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
TFR2
NM_003227.4 synonymous
NM_003227.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.73
Genes affected
TFR2 (HGNC:11762): (transferrin receptor 2) This gene encodes a single-pass type II membrane protein, which is a member of the transferrin receptor-like family. This protein mediates cellular uptake of transferrin-bound iron, and may be involved in iron metabolism, hepatocyte function and erythrocyte differentiation. Mutations in this gene have been associated with hereditary hemochromatosis type III. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 7-100620863-G-A is Benign according to our data. Variant chr7-100620863-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 755472.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.73 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.2400C>T | p.Asn800= | synonymous_variant | 18/18 | ENST00000223051.8 | |
TFR2 | NM_001206855.3 | c.1887C>T | p.Asn629= | synonymous_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFR2 | ENST00000223051.8 | c.2400C>T | p.Asn800= | synonymous_variant | 18/18 | 1 | NM_003227.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251114Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135764
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727106
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74382
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hemochromatosis type 3 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2020 | - - |
Hereditary hemochromatosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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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