chr4-139889909-TTGCTGCTGC-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_018717.5(MAML3):c.1518_1526delGCAGCAGCA(p.Gln507_Gln509del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00707 in 1,475,070 control chromosomes in the GnomAD database, including 339 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.077 ( 138 hom., cov: 0)
Exomes 𝑓: 0.0047 ( 201 hom. )
Consequence
MAML3
NM_018717.5 disruptive_inframe_deletion
NM_018717.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.00
Genes affected
MAML3 (HGNC:16272): (mastermind like transcriptional coactivator 3) Enables transcription coactivator activity. Involved in Notch signaling pathway and positive regulation of transcription by RNA polymerase II. Located in nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAML3 | NM_018717.5 | c.1518_1526delGCAGCAGCA | p.Gln507_Gln509del | disruptive_inframe_deletion | Exon 2 of 5 | ENST00000509479.6 | NP_061187.3 | |
MAML3 | XM_047415929.1 | c.1518_1526delGCAGCAGCA | p.Gln507_Gln509del | disruptive_inframe_deletion | Exon 2 of 5 | XP_047271885.1 | ||
MAML3 | XM_047415930.1 | c.1518_1526delGCAGCAGCA | p.Gln507_Gln509del | disruptive_inframe_deletion | Exon 2 of 3 | XP_047271886.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAML3 | ENST00000509479.6 | c.1518_1526delGCAGCAGCA | p.Gln507_Gln509del | disruptive_inframe_deletion | Exon 2 of 5 | 1 | NM_018717.5 | ENSP00000421180.1 | ||
MAML3 | ENST00000502696.1 | c.109-159251_109-159243delGCAGCAGCA | intron_variant | Intron 1 of 3 | 2 | ENSP00000422783.1 |
Frequencies
GnomAD3 genomes AF: 0.0773 AC: 3689AN: 47722Hom.: 138 Cov.: 0
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GnomAD3 exomes AF: 0.00916 AC: 1567AN: 171060Hom.: 48 AF XY: 0.00801 AC XY: 750AN XY: 93608
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GnomAD4 exome AF: 0.00471 AC: 6728AN: 1427260Hom.: 201 AF XY: 0.00444 AC XY: 3143AN XY: 707132
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GnomAD4 genome AF: 0.0773 AC: 3696AN: 47810Hom.: 138 Cov.: 0 AF XY: 0.0733 AC XY: 1721AN XY: 23484
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at