6-51616037-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_138694.4(PKHD1):c.*3044A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 152,210 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_138694.4 3_prime_UTR
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 |
---|---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117 | c.*3044A>T | 3_prime_UTR_variant | Exon 67 of 67 | 1 | NM_138694.4 | ENSP00000360158.3 | |||
ENSG00000228689 | ENST00000454361.1 | n.81-6318T>A | intron_variant | Intron 1 of 1 | 3 | |||||
ENSG00000228689 | ENST00000589278.6 | n.811-6323T>A | intron_variant | Intron 2 of 2 | 5 | |||||
ENSG00000228689 | ENST00000650088.1 | n.221+5605T>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.0175 AC: 2663AN: 152092Hom.: 36 Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome AF: 0.0175 AC: 2665AN: 152210Hom.: 38 Cov.: 31 AF XY: 0.0169 AC XY: 1254AN XY: 74420
ClinVar
Submissions by phenotype
Autosomal recessive polycystic kidney disease Benign:1
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at