GeneBe

rs58015886

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3

The NM_018717.5(MAML3):​c.1479_1526delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA​(p.Gln494_Gln509del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000007 in 1,428,744 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

MAML3
NM_018717.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.00
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_018717.5

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAML3NM_018717.5 linkc.1479_1526delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln494_Gln509del disruptive_inframe_deletion Exon 2 of 5 ENST00000509479.6 NP_061187.3 Q96JK9Q9NPV6
MAML3XM_047415929.1 linkc.1479_1526delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln494_Gln509del disruptive_inframe_deletion Exon 2 of 5 XP_047271885.1
MAML3XM_047415930.1 linkc.1479_1526delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln494_Gln509del disruptive_inframe_deletion Exon 2 of 3 XP_047271886.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAML3ENST00000509479.6 linkc.1479_1526delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln494_Gln509del disruptive_inframe_deletion Exon 2 of 5 1 NM_018717.5 ENSP00000421180.1 Q96JK9
MAML3ENST00000502696.1 linkc.109-159290_109-159243delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA intron_variant Intron 1 of 3 2 ENSP00000422783.1 H0Y920

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.00e-7
AC:
1
AN:
1428744
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
707956
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000227
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-140811063; API