chr14-104938648-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138420.4(AHNAK2):c.16803C>A(p.Asp5601Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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.16803C>A | p.Asp5601Glu | missense_variant | 7/7 | ENST00000333244.6 | |
AHNAK2 | NM_001350929.2 | c.16503C>A | p.Asp5501Glu | missense_variant | 7/7 | ||
AHNAK2 | XM_024449463.2 | c.16503C>A | p.Asp5501Glu | missense_variant | 7/7 | ||
AHNAK2 | XM_047430904.1 | c.16503C>A | p.Asp5501Glu | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHNAK2 | ENST00000333244.6 | c.16803C>A | p.Asp5601Glu | missense_variant | 7/7 | 5 | NM_138420.4 | P1 | |
AHNAK2 | ENST00000557457.1 | c.1797C>A | p.Asp599Glu | missense_variant | 3/3 | 1 | |||
AHNAK2 | ENST00000555122.1 | n.16931C>A | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245360Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133274
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460022Hom.: 0 Cov.: 74 AF XY: 0.00000138 AC XY: 1AN XY: 726076
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.16803C>A (p.D5601E) alteration is located in exon 7 (coding exon 7) of the AHNAK2 gene. This alteration results from a C to A substitution at nucleotide position 16803, causing the aspartic acid (D) at amino acid position 5601 to be replaced by a glutamic acid (E). 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