rs7671281
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_031889.3(ENAM):āc.1943T>Cā(p.Ile648Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 1,613,738 control chromosomes in the GnomAD database, including 9,962 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_031889.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENAM | NM_031889.3 | c.1943T>C | p.Ile648Thr | missense_variant | 9/9 | ENST00000396073.4 | |
ENAM | NM_001368133.1 | c.1289T>C | p.Ile430Thr | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENAM | ENST00000396073.4 | c.1943T>C | p.Ile648Thr | missense_variant | 9/9 | 1 | NM_031889.3 | P1 | |
ENST00000472903.5 | n.99+5526T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24529AN: 151924Hom.: 4479 Cov.: 31
GnomAD3 exomes AF: 0.0799 AC: 20030AN: 250758Hom.: 2130 AF XY: 0.0708 AC XY: 9601AN XY: 135522
GnomAD4 exome AF: 0.0538 AC: 78638AN: 1461696Hom.: 5455 Cov.: 34 AF XY: 0.0526 AC XY: 38270AN XY: 727144
GnomAD4 genome ? AF: 0.162 AC: 24606AN: 152042Hom.: 4507 Cov.: 31 AF XY: 0.159 AC XY: 11824AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Amelogenesis imperfecta Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at