chr5-141573477-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005219.5(DIAPH1):c.2358+15C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000915 in 1,321,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005219.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIAPH1 | ENST00000389054.8 | c.2358+15C>G | intron_variant | Intron 16 of 27 | 5 | NM_005219.5 | ENSP00000373706.4 | |||
DIAPH1 | ENST00000518047.5 | c.2331+15C>G | intron_variant | Intron 15 of 26 | 5 | ENSP00000428268.2 | ||||
DIAPH1 | ENST00000647433.1 | c.2358+15C>G | intron_variant | Intron 16 of 28 | ENSP00000494675.1 |
Frequencies
GnomAD3 genomes AF: 0.000377 AC: 56AN: 148454Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000742 AC: 18AN: 242530Hom.: 0 AF XY: 0.0000453 AC XY: 6AN XY: 132510
GnomAD4 exome AF: 0.0000554 AC: 65AN: 1173456Hom.: 0 Cov.: 38 AF XY: 0.0000489 AC XY: 29AN XY: 593456
GnomAD4 genome AF: 0.000377 AC: 56AN: 148542Hom.: 0 Cov.: 28 AF XY: 0.000276 AC XY: 20AN XY: 72460
ClinVar
Submissions by phenotype
not specified Benign:1
2358+15C>G in Intron 16 of DIAPH1: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus se quence and has been identified in 0.1% (4/2940) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.was hington.edu/EVS). -
Autosomal dominant nonsyndromic hearing loss 1;C5567650:Progressive microcephaly-seizures-cortical blindness-developmental delay syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at