chr10-95225348-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207321.3(ACSM6):c.1259G>A(p.Arg420His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,551,472 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_207321.3 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 |
---|---|---|---|---|---|---|---|
ACSM6 | NM_207321.3 | c.1259G>A | p.Arg420His | missense_variant | 10/11 | ENST00000394005.4 | |
LOC107984257 | XR_007062253.1 | n.347+200C>T | intron_variant, non_coding_transcript_variant | ||||
ACSM6 | XM_047424638.1 | c.1259G>A | p.Arg420His | missense_variant | 10/10 | ||
ACSM6 | XM_047424639.1 | c.1259G>A | p.Arg420His | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSM6 | ENST00000394005.4 | c.1259G>A | p.Arg420His | missense_variant | 10/11 | 5 | NM_207321.3 | P1 | |
ACSM6 | ENST00000327739.7 | c.*699G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 | ||||
ACSM6 | ENST00000404473.6 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000108 AC: 17AN: 156764Hom.: 0 AF XY: 0.000120 AC XY: 10AN XY: 83010
GnomAD4 exome AF: 0.0000722 AC: 101AN: 1399180Hom.: 0 Cov.: 30 AF XY: 0.0000623 AC XY: 43AN XY: 690100
GnomAD4 genome ? AF: 0.000473 AC: 72AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000510 AC XY: 38AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.1259G>A (p.R420H) alteration is located in exon 10 (coding exon 9) of the ACSM6 gene. This alteration results from a G to A substitution at nucleotide position 1259, causing the arginine (R) at amino acid position 420 to be replaced by a histidine (H). 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