chr18-35070330-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014268.4(MAPRE2):c.250+8A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000988 in 1,586,276 control chromosomes in the GnomAD database, including 27 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_014268.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPRE2 | NM_014268.4 | c.250+8A>T | splice_region_variant, intron_variant | ENST00000300249.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPRE2 | ENST00000300249.10 | c.250+8A>T | splice_region_variant, intron_variant | 1 | NM_014268.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00146 AC: 222AN: 152214Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00239 AC: 541AN: 225990Hom.: 10 AF XY: 0.00224 AC XY: 274AN XY: 122256
GnomAD4 exome AF: 0.000939 AC: 1346AN: 1433944Hom.: 18 Cov.: 29 AF XY: 0.000949 AC XY: 676AN XY: 712186
GnomAD4 genome AF: 0.00146 AC: 222AN: 152332Hom.: 9 Cov.: 32 AF XY: 0.00141 AC XY: 105AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at