2-62859208-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001142616.3(EHBP1):c.674A>C(p.Lys225Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000236 in 1,612,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. K225R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142616.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EHBP1 | NM_001142616.3 | c.674A>C | p.Lys225Thr | missense_variant | 8/23 | ENST00000431489.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EHBP1 | ENST00000431489.6 | c.674A>C | p.Lys225Thr | missense_variant | 8/23 | 1 | NM_001142616.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251086Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135686
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459720Hom.: 0 Cov.: 30 AF XY: 0.00000964 AC XY: 7AN XY: 726084
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2023 | The c.779A>C (p.K260T) alteration is located in exon 9 (coding exon 8) of the EHBP1 gene. This alteration results from a A to C substitution at nucleotide position 779, causing the lysine (K) at amino acid position 260 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