chr14-104938773-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138420.4(AHNAK2):c.16678G>A(p.Asp5560Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.16678G>A | p.Asp5560Asn | missense_variant | 7/7 | ENST00000333244.6 | |
AHNAK2 | NM_001350929.2 | c.16378G>A | p.Asp5460Asn | missense_variant | 7/7 | ||
AHNAK2 | XM_024449463.2 | c.16378G>A | p.Asp5460Asn | missense_variant | 7/7 | ||
AHNAK2 | XM_047430904.1 | c.16378G>A | p.Asp5460Asn | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHNAK2 | ENST00000333244.6 | c.16678G>A | p.Asp5560Asn | missense_variant | 7/7 | 5 | NM_138420.4 | P1 | |
AHNAK2 | ENST00000557457.1 | c.1672G>A | p.Asp558Asn | missense_variant | 3/3 | 1 | |||
AHNAK2 | ENST00000555122.1 | n.16806G>A | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 18AN: 248952Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135152
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461624Hom.: 0 Cov.: 73 AF XY: 0.0000371 AC XY: 27AN XY: 727084
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.16678G>A (p.D5560N) alteration is located in exon 7 (coding exon 7) of the AHNAK2 gene. This alteration results from a G to A substitution at nucleotide position 16678, causing the aspartic acid (D) at amino acid position 5560 to be replaced by an asparagine (N). 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