chr5-141577472-T-A
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_005219.5(DIAPH1):c.1280+3A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005219.5 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- DIAPH1-related sensorineural hearing loss-thrombocytopenia syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- autosomal dominant nonsyndromic hearing loss 1Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia
- progressive microcephaly-seizures-cortical blindness-developmental delay syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIAPH1 | ENST00000389054.8 | c.1280+3A>T | splice_region_variant, intron_variant | Intron 12 of 27 | 5 | NM_005219.5 | ENSP00000373706.4 | |||
DIAPH1 | ENST00000518047.5 | c.1253+3A>T | splice_region_variant, intron_variant | Intron 11 of 26 | 5 | ENSP00000428268.2 | ||||
DIAPH1 | ENST00000647433.1 | c.1280+3A>T | splice_region_variant, intron_variant | Intron 12 of 28 | ENSP00000494675.1 | |||||
DIAPH1 | ENST00000523100.5 | n.*510A>T | downstream_gene_variant | 5 | ENSP00000428208.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at