rs7652072
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_000187.4(HGD):c.283-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,606,428 control chromosomes in the GnomAD database, including 13 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_000187.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGD | NM_000187.4 | c.283-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000283871.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGD | ENST00000283871.10 | c.283-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000187.4 | P1 | |||
HGD | ENST00000476082.2 | c.160-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
HGD | ENST00000485313.5 | n.391-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 | |||||
HGD | ENST00000488183.5 | n.541-9C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00489 AC: 741AN: 151592Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00148 AC: 364AN: 246396Hom.: 1 AF XY: 0.00116 AC XY: 154AN XY: 133110
GnomAD4 exome AF: 0.000651 AC: 947AN: 1454718Hom.: 6 Cov.: 29 AF XY: 0.000599 AC XY: 434AN XY: 724140
GnomAD4 genome ? AF: 0.00489 AC: 742AN: 151710Hom.: 7 Cov.: 32 AF XY: 0.00447 AC XY: 331AN XY: 74132
ClinVar
Submissions by phenotype
Alkaptonuria Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at