2-62707274-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001142616.3(EHBP1):c.83T>C(p.Met28Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M28V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142616.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHBP1 | NM_001142616.3 | c.83T>C | p.Met28Thr | missense_variant | 2/23 | ENST00000431489.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHBP1 | ENST00000431489.6 | c.83T>C | p.Met28Thr | missense_variant | 2/23 | 1 | NM_001142616.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251488Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135920
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461648Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727146
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.83T>C (p.M28T) alteration is located in exon 2 (coding exon 1) of the EHBP1 gene. This alteration results from a T to C substitution at nucleotide position 83, causing the methionine (M) at amino acid position 28 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at