chr14-104938734-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138420.4(AHNAK2):c.16717C>T(p.Pro5573Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,694 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P5573Q) has been classified 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.16717C>T | p.Pro5573Ser | missense_variant | 7/7 | ENST00000333244.6 | |
AHNAK2 | NM_001350929.2 | c.16417C>T | p.Pro5473Ser | missense_variant | 7/7 | ||
AHNAK2 | XM_024449463.2 | c.16417C>T | p.Pro5473Ser | missense_variant | 7/7 | ||
AHNAK2 | XM_047430904.1 | c.16417C>T | p.Pro5473Ser | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHNAK2 | ENST00000333244.6 | c.16717C>T | p.Pro5573Ser | missense_variant | 7/7 | 5 | NM_138420.4 | P1 | |
AHNAK2 | ENST00000557457.1 | c.1711C>T | p.Pro571Ser | missense_variant | 3/3 | 1 | |||
AHNAK2 | ENST00000555122.1 | n.16845C>T | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152158Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000113 AC: 28AN: 248578Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135012
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461536Hom.: 0 Cov.: 73 AF XY: 0.0000344 AC XY: 25AN XY: 727022
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152158Hom.: 1 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.16717C>T (p.P5573S) alteration is located in exon 7 (coding exon 7) of the AHNAK2 gene. This alteration results from a C to T substitution at nucleotide position 16717, causing the proline (P) at amino acid position 5573 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