chr1-225839847-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001136018.4(EPHX1):c.741C>T(p.His247His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 1,613,916 control chromosomes in the GnomAD database, including 3,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001136018.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHX1 | ENST00000272167.10 | c.741C>T | p.His247His | synonymous_variant | Exon 6 of 9 | 1 | NM_001136018.4 | ENSP00000272167.5 | ||
EPHX1 | ENST00000366837.5 | c.741C>T | p.His247His | synonymous_variant | Exon 6 of 9 | 1 | ENSP00000355802.4 | |||
EPHX1 | ENST00000614058.4 | c.741C>T | p.His247His | synonymous_variant | Exon 6 of 9 | 1 | ENSP00000480004.1 |
Frequencies
GnomAD3 genomes AF: 0.0533 AC: 8112AN: 152184Hom.: 240 Cov.: 32
GnomAD3 exomes AF: 0.0524 AC: 13171AN: 251364Hom.: 415 AF XY: 0.0533 AC XY: 7235AN XY: 135862
GnomAD4 exome AF: 0.0608 AC: 88818AN: 1461614Hom.: 2944 Cov.: 32 AF XY: 0.0609 AC XY: 44296AN XY: 727122
GnomAD4 genome AF: 0.0532 AC: 8104AN: 152302Hom.: 240 Cov.: 32 AF XY: 0.0527 AC XY: 3928AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
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EPHX1-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