6-116462083-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001010919.3(CALHM6):c.154G>A(p.Gly52Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000168 in 1,546,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010919.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALHM6 | NM_001010919.3 | c.154G>A | p.Gly52Ser | missense_variant | Exon 2 of 3 | ENST00000368605.3 | NP_001010919.1 | |
CALHM6 | XM_011535845.4 | c.154G>A | p.Gly52Ser | missense_variant | Exon 1 of 2 | XP_011534147.1 | ||
CALHM6 | NM_001276460.2 | c.9+654G>A | intron_variant | Intron 1 of 1 | NP_001263389.1 | |||
CALHM6-AS1 | NR_174951.1 | n.87-889C>T | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CALHM6 | ENST00000368605.3 | c.154G>A | p.Gly52Ser | missense_variant | Exon 2 of 3 | 5 | NM_001010919.3 | ENSP00000357594.1 | ||
ENSG00000285446 | ENST00000644499.1 | c.767-1200G>A | intron_variant | Intron 3 of 3 | ENSP00000495266.1 | |||||
CALHM6 | ENST00000368606.7 | c.9+654G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000357595.3 | ||||
CALHM6-AS1 | ENST00000476099.1 | n.75-889C>T | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152090Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000675 AC: 10AN: 148178Hom.: 0 AF XY: 0.0000253 AC XY: 2AN XY: 78946
GnomAD4 exome AF: 0.0000165 AC: 23AN: 1394390Hom.: 0 Cov.: 33 AF XY: 0.00000727 AC XY: 5AN XY: 687762
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154G>A (p.G52S) alteration is located in exon 2 (coding exon 1) of the FAM26F gene. This alteration results from a G to A substitution at nucleotide position 154, causing the glycine (G) at amino acid position 52 to be replaced by a serine (S). 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