5-148133895-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006846.4(SPINK5):c.3186+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00176 in 1,613,694 control chromosomes in the GnomAD database, including 42 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_006846.4 splice_region, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPINK5 | NM_006846.4 | c.3186+8C>T | splice_region_variant, intron_variant | ENST00000256084.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPINK5 | ENST00000256084.8 | c.3186+8C>T | splice_region_variant, intron_variant | 1 | NM_006846.4 | P2 | |||
SPINK5 | ENST00000359874.7 | c.3276+8C>T | splice_region_variant, intron_variant | 1 | A2 | ||||
FBXO38-DT | ENST00000667608.1 | n.1257-40153G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00977 AC: 1486AN: 152118Hom.: 28 Cov.: 32
GnomAD3 exomes AF: 0.00236 AC: 587AN: 249242Hom.: 8 AF XY: 0.00177 AC XY: 239AN XY: 135248
GnomAD4 exome AF: 0.000921 AC: 1346AN: 1461458Hom.: 14 Cov.: 31 AF XY: 0.000806 AC XY: 586AN XY: 727068
GnomAD4 genome AF: 0.00978 AC: 1489AN: 152236Hom.: 28 Cov.: 32 AF XY: 0.00930 AC XY: 692AN XY: 74432
ClinVar
Submissions by phenotype
Ichthyosis linearis circumflexa Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Netherton syndrome Benign:1
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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at