NM_003227.4:c.1767+7C>G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003227.4(TFR2):c.1767+7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,614,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003227.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.1767+7C>G | splice_region_variant, intron_variant | Intron 15 of 17 | ENST00000223051.8 | NP_003218.2 | ||
TFR2 | NM_001206855.3 | c.1254+7C>G | splice_region_variant, intron_variant | Intron 12 of 14 | NP_001193784.1 | |||
LOC124901709 | XR_007060454.1 | n.434-3586G>C | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251060Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135712
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461822Hom.: 0 Cov.: 40 AF XY: 0.0000179 AC XY: 13AN XY: 727200
GnomAD4 genome AF: 0.000190 AC: 29AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74470
ClinVar
Submissions by phenotype
Hemochromatosis type 3 Benign:1
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Hereditary hemochromatosis Benign:1
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TFR2-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