chrX-44232527-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025184.4(EFHC2):c.1574A>T(p.Asn525Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000937 in 1,066,898 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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. N525S) has been classified as Uncertain significance.
Frequency
Consequence
NM_025184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHC2 | NM_025184.4 | c.1574A>T | p.Asn525Ile | missense_variant | 10/15 | ENST00000420999.2 | |
EFHC2 | XM_047442535.1 | c.1574A>T | p.Asn525Ile | missense_variant | 10/14 | ||
EFHC2 | XM_047442536.1 | c.1574A>T | p.Asn525Ile | missense_variant | 10/15 | ||
EFHC2 | XM_006724562.3 | c.986A>T | p.Asn329Ile | missense_variant | 9/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC2 | ENST00000420999.2 | c.1574A>T | p.Asn525Ile | missense_variant | 10/15 | 1 | NM_025184.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 9.37e-7 AC: 1AN: 1066898Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 341374
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Feb 07, 2024 | Gene of Uncertain Significance - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.