chr7-100627570-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003227.4(TFR2):c.1767+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00729 in 1,614,130 control chromosomes in the GnomAD database, including 72 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_003227.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.1767+7C>T | splice_region_variant, intron_variant | Intron 15 of 17 | ENST00000223051.8 | NP_003218.2 | ||
TFR2 | NM_001206855.3 | c.1254+7C>T | splice_region_variant, intron_variant | Intron 12 of 14 | NP_001193784.1 | |||
LOC124901709 | XR_007060454.1 | n.434-3586G>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00594 AC: 904AN: 152194Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00703 AC: 1766AN: 251060Hom.: 17 AF XY: 0.00735 AC XY: 998AN XY: 135712
GnomAD4 exome AF: 0.00743 AC: 10861AN: 1461818Hom.: 66 Cov.: 40 AF XY: 0.00767 AC XY: 5575AN XY: 727200
GnomAD4 genome AF: 0.00593 AC: 903AN: 152312Hom.: 6 Cov.: 33 AF XY: 0.00553 AC XY: 412AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:3
- -
- -
TFR2: BP4, BS1, BS2 -
Hemochromatosis type 3 Benign:2
- -
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 rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Hereditary hemochromatosis Benign:1
- -
TFR2-related disorder Benign:1
This variant is classified as 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