chr1-147647445-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016361.5(ACP6):āc.1265T>Cā(p.Met422Thr) 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 1,461,782 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 (ā ).
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.1265T>C | p.Met422Thr | missense_variant | 10/10 | ENST00000583509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACP6 | ENST00000583509.7 | c.1265T>C | p.Met422Thr | missense_variant | 10/10 | 1 | NM_016361.5 | P1 | |
ACP6 | ENST00000613673.4 | n.4487T>C | non_coding_transcript_exon_variant | 8/8 | 1 | ||||
ACP6 | ENST00000609196.5 | c.460+2698T>C | intron_variant | 3 | |||||
ACP6 | ENST00000460583.1 | n.828T>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251170Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135746
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461782Hom.: 0 Cov.: 29 AF XY: 0.00000275 AC XY: 2AN XY: 727194
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2022 | The c.1265T>C (p.M422T) alteration is located in exon 10 (coding exon 10) of the ACP6 gene. This alteration results from a T to C substitution at nucleotide position 1265, causing the methionine (M) at amino acid position 422 to be replaced by a threonine (T). 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