chrX-15809200-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005089.4(ZRSR2):c.439T>C(p.Leu147=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000377 in 1,193,471 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 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 Likely benign (★).
Frequency
Consequence
NM_005089.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZRSR2 | NM_005089.4 | c.439T>C | p.Leu147= | splice_region_variant, synonymous_variant | 7/11 | ENST00000307771.8 | |
ZRSR2 | XM_011545589.4 | c.508T>C | p.Leu170= | splice_region_variant, synonymous_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZRSR2 | ENST00000307771.8 | c.439T>C | p.Leu147= | splice_region_variant, synonymous_variant | 7/11 | 1 | NM_005089.4 | P2 | |
ZRSR2 | ENST00000684799.1 | c.361T>C | p.Leu121= | splice_region_variant, synonymous_variant | 6/11 | A2 | |||
ZRSR2 | ENST00000690252.1 | c.439T>C | p.Leu147= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 7/13 | ||||
ZRSR2 | ENST00000691502.1 | c.439T>C | p.Leu147= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 7/13 |
Frequencies
GnomAD3 genomes ? AF: 0.0000356 AC: 4AN: 112509Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34669
GnomAD3 exomes AF: 0.0000768 AC: 14AN: 182279Hom.: 0 AF XY: 0.0000749 AC XY: 5AN XY: 66775
GnomAD4 exome AF: 0.0000379 AC: 41AN: 1080909Hom.: 0 Cov.: 27 AF XY: 0.0000401 AC XY: 14AN XY: 348779
GnomAD4 genome ? AF: 0.0000355 AC: 4AN: 112562Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34732
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at