chrX-107904072-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012216.4(MID2):c.924+7C>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 0.00018 in 1,098,627 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 51 hemizygotes in GnomAD. 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_012216.4 splice_region, 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 |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.924+7C>T | splice_region_variant, intron_variant | ENST00000262843.11 | |||
LOC101928335 | NR_110395.1 | n.327-7712G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.924+7C>T | splice_region_variant, intron_variant | 1 | NM_012216.4 | ||||
ENST00000663626.2 | n.556+28958G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000867 AC: 97AN: 111834Hom.: 0 Cov.: 23 AF XY: 0.000735 AC XY: 25AN XY: 34032
GnomAD3 exomes AF: 0.000183 AC: 33AN: 180231Hom.: 0 AF XY: 0.000138 AC XY: 9AN XY: 65247
GnomAD4 exome AF: 0.000102 AC: 101AN: 986740Hom.: 0 Cov.: 21 AF XY: 0.0000930 AC XY: 26AN XY: 279596
GnomAD4 genome ? AF: 0.000867 AC: 97AN: 111887Hom.: 0 Cov.: 23 AF XY: 0.000733 AC XY: 25AN XY: 34095
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