6-116558047-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001366078.2(CALHM4):c.781G>A(p.Val261Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,614,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366078.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALHM4 | NM_001366078.2 | c.781G>A | p.Val261Ile | missense_variant | 2/2 | ENST00000368596.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALHM4 | ENST00000368596.4 | c.781G>A | p.Val261Ile | missense_variant | 2/2 | 5 | NM_001366078.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251426Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135882
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727232
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.223G>A (p.V75I) alteration is located in exon 3 (coding exon 1) of the FAM26D gene. This alteration results from a G to A substitution at nucleotide position 223, causing the valine (V) at amino acid position 75 to be replaced by an isoleucine (I). 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