chr10-21614831-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001195626.3(MLLT10):c.510C>T(p.Cys170=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,609,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001195626.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLLT10 | NM_001195626.3 | c.510C>T | p.Cys170= | splice_region_variant, synonymous_variant | 7/23 | ENST00000307729.12 | NP_001182555.1 | |
MLLT10 | NM_004641.4 | c.510C>T | p.Cys170= | splice_region_variant, synonymous_variant | 7/24 | NP_004632.1 | ||
MLLT10 | NM_001324297.2 | c.-362C>T | splice_region_variant, 5_prime_UTR_variant | 8/25 | NP_001311226.1 | |||
MLLT10 | NR_136736.2 | n.977C>T | splice_region_variant, non_coding_transcript_exon_variant | 8/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLLT10 | ENST00000307729.12 | c.510C>T | p.Cys170= | splice_region_variant, synonymous_variant | 7/23 | 1 | NM_001195626.3 | ENSP00000307411 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151964Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247824Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133864
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1457204Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 724802
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151964Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74214
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at