1-204538313-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002393.5(MDM4):c.511+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0007 in 1,497,784 control chromosomes in the GnomAD database, including 8 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_002393.5 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MDM4 | NM_002393.5 | c.511+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000367182.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MDM4 | ENST00000367182.8 | c.511+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_002393.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00307 AC: 467AN: 152190Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000857 AC: 213AN: 248470Hom.: 0 AF XY: 0.000714 AC XY: 96AN XY: 134416
GnomAD4 exome AF: 0.000427 AC: 574AN: 1345476Hom.: 6 Cov.: 21 AF XY: 0.000386 AC XY: 261AN XY: 675800
GnomAD4 genome AF: 0.00312 AC: 475AN: 152308Hom.: 2 Cov.: 32 AF XY: 0.00285 AC XY: 212AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at