chr10-21673634-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001195626.3(MLLT10):c.1336C>T(p.Pro446Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001195626.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLLT10 | NM_001195626.3 | c.1336C>T | p.Pro446Ser | missense_variant | 11/23 | ENST00000307729.12 | |
MLLT10 | NM_004641.4 | c.1336C>T | p.Pro446Ser | missense_variant | 11/24 | ||
MLLT10 | NM_001324297.2 | c.601C>T | p.Pro201Ser | missense_variant | 13/25 | ||
MLLT10 | NR_136736.2 | n.1803C>T | non_coding_transcript_exon_variant | 12/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT10 | ENST00000307729.12 | c.1336C>T | p.Pro446Ser | missense_variant | 11/23 | 1 | NM_001195626.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250952Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135678
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461752Hom.: 0 Cov.: 35 AF XY: 0.00000688 AC XY: 5AN XY: 727170
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152214Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.1336C>T (p.P446S) alteration is located in exon 10 (coding exon 10) of the MLLT10 gene. This alteration results from a C to T substitution at nucleotide position 1336, causing the proline (P) at amino acid position 446 to be replaced by a serine (S). 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