14-104939027-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138420.4(AHNAK2):āc.16424A>Gā(p.Gln5475Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,609,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_138420.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHNAK2 | NM_138420.4 | c.16424A>G | p.Gln5475Arg | missense_variant | 7/7 | ENST00000333244.6 | |
AHNAK2 | NM_001350929.2 | c.16124A>G | p.Gln5375Arg | missense_variant | 7/7 | ||
AHNAK2 | XM_024449463.2 | c.16124A>G | p.Gln5375Arg | missense_variant | 7/7 | ||
AHNAK2 | XM_047430904.1 | c.16124A>G | p.Gln5375Arg | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHNAK2 | ENST00000333244.6 | c.16424A>G | p.Gln5475Arg | missense_variant | 7/7 | 5 | NM_138420.4 | P1 | |
AHNAK2 | ENST00000557457.1 | c.1418A>G | p.Gln473Arg | missense_variant | 3/3 | 1 | |||
AHNAK2 | ENST00000555122.1 | n.16552A>G | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239662Hom.: 0 AF XY: 0.00000769 AC XY: 1AN XY: 130114
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1457044Hom.: 0 Cov.: 73 AF XY: 0.00000966 AC XY: 7AN XY: 724362
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2023 | The c.16424A>G (p.Q5475R) alteration is located in exon 7 (coding exon 7) of the AHNAK2 gene. This alteration results from a A to G substitution at nucleotide position 16424, causing the glutamine (Q) at amino acid position 5475 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