10-102890629-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020682.4(AS3MT):āc.971T>Cā(p.Ile324Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,476 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 (ā ).
Frequency
Consequence
NM_020682.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AS3MT | NM_020682.4 | c.971T>C | p.Ile324Thr | missense_variant | 10/11 | ENST00000369880.8 | NP_065733.2 | |
BORCS7-ASMT | NR_037644.1 | n.1376T>C | non_coding_transcript_exon_variant | 14/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AS3MT | ENST00000369880.8 | c.971T>C | p.Ile324Thr | missense_variant | 10/11 | 1 | NM_020682.4 | ENSP00000358896 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152118Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 248968Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135104
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461358Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726980
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152118Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | The c.971T>C (p.I324T) alteration is located in exon 10 (coding exon 10) of the AS3MT gene. This alteration results from a T to C substitution at nucleotide position 971, causing the isoleucine (I) at amino acid position 324 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