10-95212009-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207321.3(ACSM6):c.887C>T(p.Thr296Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,970 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_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.887C>T | p.Thr296Ile | missense_variant | 6/11 | ENST00000394005.4 | |
LOC107984257 | XR_007062253.1 | n.347+13539G>A | intron_variant, non_coding_transcript_variant | ||||
ACSM6 | XM_047424638.1 | c.887C>T | p.Thr296Ile | missense_variant | 6/10 | ||
ACSM6 | XM_047424639.1 | c.887C>T | p.Thr296Ile | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSM6 | ENST00000394005.4 | c.887C>T | p.Thr296Ile | missense_variant | 6/11 | 5 | NM_207321.3 | P1 | |
ACSM6 | ENST00000404473.6 | c.*710C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/10 | 1 | ||||
ACSM6 | ENST00000327739.7 | c.*451C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251190Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135748
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727200
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.887C>T (p.T296I) alteration is located in exon 6 (coding exon 5) of the ACSM6 gene. This alteration results from a C to T substitution at nucleotide position 887, causing the threonine (T) at amino acid position 296 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