NM_032117.4:c.4-5T>G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_032117.4(MND1):c.4-5T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000715 in 1,585,806 control chromosomes in the GnomAD database, including 9 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_032117.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MND1 | ENST00000240488.8 | c.4-5T>G | splice_region_variant, intron_variant | Intron 1 of 7 | 1 | NM_032117.4 | ENSP00000240488.3 | |||
ENSG00000288637 | ENST00000675079.1 | c.2095-5T>G | splice_region_variant, intron_variant | Intron 11 of 17 | ENSP00000502677.1 |
Frequencies
GnomAD3 genomes AF: 0.00368 AC: 560AN: 152212Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000998 AC: 231AN: 231472Hom.: 3 AF XY: 0.000719 AC XY: 90AN XY: 125220
GnomAD4 exome AF: 0.000399 AC: 572AN: 1433476Hom.: 6 Cov.: 28 AF XY: 0.000341 AC XY: 243AN XY: 712622
GnomAD4 genome AF: 0.00369 AC: 562AN: 152330Hom.: 3 Cov.: 32 AF XY: 0.00380 AC XY: 283AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at