7-16600820-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020319.3(ANKMY2):c.1267G>A(p.Glu423Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,613,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020319.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKMY2 | NM_020319.3 | c.1267G>A | p.Glu423Lys | missense_variant | Exon 10 of 10 | ENST00000306999.7 | NP_064715.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKMY2 | ENST00000306999.7 | c.1267G>A | p.Glu423Lys | missense_variant | Exon 10 of 10 | 1 | NM_020319.3 | ENSP00000303570.2 | ||
ANKMY2 | ENST00000447802.3 | n.*353G>A | non_coding_transcript_exon_variant | Exon 11 of 11 | 2 | ENSP00000392259.1 | ||||
ANKMY2 | ENST00000447802.3 | n.*353G>A | 3_prime_UTR_variant | Exon 11 of 11 | 2 | ENSP00000392259.1 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250678Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135506
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461528Hom.: 0 Cov.: 33 AF XY: 0.0000550 AC XY: 40AN XY: 727062
GnomAD4 genome AF: 0.000604 AC: 92AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.000671 AC XY: 50AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1267G>A (p.E423K) alteration is located in exon 10 (coding exon 10) of the ANKMY2 gene. This alteration results from a G to A substitution at nucleotide position 1267, causing the glutamic acid (E) at amino acid position 423 to be replaced by a lysine (K). 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