chr1-147647504-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016361.5(ACP6):c.1206G>A(p.Met402Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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. M402V) has been classified as Benign.
Frequency
Consequence
NM_016361.5 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 |
---|---|---|---|---|---|---|---|
ACP6 | NM_016361.5 | c.1206G>A | p.Met402Ile | missense_variant | 10/10 | ENST00000583509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACP6 | ENST00000583509.7 | c.1206G>A | p.Met402Ile | missense_variant | 10/10 | 1 | NM_016361.5 | P1 | |
ACP6 | ENST00000613673.4 | n.4428G>A | non_coding_transcript_exon_variant | 8/8 | 1 | ||||
ACP6 | ENST00000609196.5 | c.460+2639G>A | intron_variant | 3 | |||||
ACP6 | ENST00000460583.1 | n.769G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251384Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135868
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461828Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727224
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 17, 2023 | The c.1206G>A (p.M402I) alteration is located in exon 10 (coding exon 10) of the ACP6 gene. This alteration results from a G to A substitution at nucleotide position 1206, causing the methionine (M) at amino acid position 402 to be replaced by an isoleucine (I). 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