NM_001006657.2:c.*3268C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001006657.2(WDR35):c.*3268C>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 0.0165 in 152,176 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001006657.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR35 | NM_001006657.2 | c.*3268C>T | 3_prime_UTR_variant | Exon 28 of 28 | ENST00000345530.8 | NP_001006658.1 | ||
WDR35 | NM_020779.4 | c.*3268C>T | 3_prime_UTR_variant | Exon 27 of 27 | ENST00000281405.9 | NP_065830.2 | ||
WDR35 | XM_011533007.3 | c.*3268C>T | 3_prime_UTR_variant | Exon 17 of 17 | XP_011531309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR35 | ENST00000345530 | c.*3268C>T | 3_prime_UTR_variant | Exon 28 of 28 | 1 | NM_001006657.2 | ENSP00000314444.5 | |||
WDR35 | ENST00000281405 | c.*3268C>T | 3_prime_UTR_variant | Exon 27 of 27 | 1 | NM_020779.4 | ENSP00000281405.5 |
Frequencies
GnomAD3 genomes AF: 0.0165 AC: 2505AN: 152058Hom.: 72 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome AF: 0.0165 AC: 2512AN: 152176Hom.: 72 Cov.: 33 AF XY: 0.0155 AC XY: 1155AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:1
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Cranioectodermal dysplasia 2 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Short-rib thoracic dysplasia 7 with or without polydactyly 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at