chr7-73596240-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_032951.3(MLXIPL):c.1971G>A(p.Ala657=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,612,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00022 ( 0 hom. )
Consequence
MLXIPL
NM_032951.3 synonymous
NM_032951.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -10.4
Genes affected
MLXIPL (HGNC:12744): (MLX interacting protein like) This gene encodes a basic helix-loop-helix leucine zipper transcription factor of the Myc/Max/Mad superfamily. This protein forms a heterodimeric complex and binds and activates, in a glucose-dependent manner, carbohydrate response element (ChoRE) motifs in the promoters of triglyceride synthesis genes. The gene is deleted in Williams-Beuren syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at chromosome 7q11.23. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
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Variant 7-73596240-C-T is Benign according to our data. Variant chr7-73596240-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 763279.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLXIPL | NM_032951.3 | c.1971G>A | p.Ala657= | synonymous_variant | 13/17 | ENST00000313375.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLXIPL | ENST00000313375.8 | c.1971G>A | p.Ala657= | synonymous_variant | 13/17 | 1 | NM_032951.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000186 AC: 28AN: 150750Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000151 AC: 38AN: 251150Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135866
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GnomAD4 exome AF: 0.000218 AC: 319AN: 1461594Hom.: 0 Cov.: 35 AF XY: 0.000219 AC XY: 159AN XY: 727086
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GnomAD4 genome ? AF: 0.000186 AC: 28AN: 150854Hom.: 0 Cov.: 30 AF XY: 0.000190 AC XY: 14AN XY: 73564
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at