5-148063984-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006846.4(SPINK5):c.-61A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00866 in 1,585,648 control chromosomes in the GnomAD database, including 1,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006846.4 5_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPINK5 | NM_006846.4 | c.-61A>C | 5_prime_UTR_variant | Exon 1 of 33 | ENST00000256084.8 | NP_006837.2 | ||
SPINK5 | NM_001127698.2 | c.-61A>C | 5_prime_UTR_variant | Exon 1 of 34 | NP_001121170.1 | |||
SPINK5 | NM_001127699.2 | c.-61A>C | 5_prime_UTR_variant | Exon 1 of 28 | NP_001121171.1 | |||
SPINK5 | XM_047416662.1 | c.-61A>C | 5_prime_UTR_variant | Exon 1 of 34 | XP_047272618.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0450 AC: 6839AN: 152130Hom.: 534 Cov.: 32
GnomAD4 exome AF: 0.00478 AC: 6852AN: 1433400Hom.: 474 Cov.: 26 AF XY: 0.00407 AC XY: 2914AN XY: 715138
GnomAD4 genome AF: 0.0452 AC: 6876AN: 152248Hom.: 538 Cov.: 32 AF XY: 0.0432 AC XY: 3213AN XY: 74446
ClinVar
Submissions by phenotype
Netherton syndrome 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. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at