17-78205121-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001010982.5(AFMID):c.496G>A(p.Gly166Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,612,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010982.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000406 AC: 10AN: 246392Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133352
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1460150Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726216
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.496G>A (p.G166R) alteration is located in exon 7 (coding exon 7) of the AFMID gene. This alteration results from a G to A substitution at nucleotide position 496, causing the glycine (G) at amino acid position 166 to be replaced by an arginine (R). 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