chr15-41900941-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000220325.9(EHD4):c.1330G>A(p.Val444Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000731 in 1,613,750 control chromosomes in the GnomAD database, including 1 homozygotes. 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. V444L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000220325.9 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EHD4 | NM_139265.4 | c.1330G>A | p.Val444Met | missense_variant | 6/6 | ENST00000220325.9 | NP_644670.1 | |
EHD4 | XM_047432408.1 | c.1066G>A | p.Val356Met | missense_variant | 6/6 | XP_047288364.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EHD4 | ENST00000220325.9 | c.1330G>A | p.Val444Met | missense_variant | 6/6 | 1 | NM_139265.4 | ENSP00000220325 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251128Hom.: 1 AF XY: 0.0000368 AC XY: 5AN XY: 135748
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461594Hom.: 1 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 727042
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.1330G>A (p.V444M) alteration is located in exon 6 (coding exon 6) of the EHD4 gene. This alteration results from a G to A substitution at nucleotide position 1330, causing the valine (V) at amino acid position 444 to be replaced by a methionine (M). 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