5-148064026-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006846.4(SPINK5):c.-19G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0086 in 1,614,022 control chromosomes in the GnomAD database, including 83 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
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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 |
---|---|---|---|---|---|---|---|---|
SPINK5 | NM_006846.4 | c.-19G>A | 5_prime_UTR_variant | Exon 1 of 33 | ENST00000256084.8 | NP_006837.2 | ||
SPINK5 | NM_001127698.2 | c.-19G>A | 5_prime_UTR_variant | Exon 1 of 34 | NP_001121170.1 | |||
SPINK5 | NM_001127699.2 | c.-19G>A | 5_prime_UTR_variant | Exon 1 of 28 | NP_001121171.1 | |||
SPINK5 | XM_047416662.1 | c.-19G>A | 5_prime_UTR_variant | Exon 1 of 34 | XP_047272618.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00640 AC: 973AN: 152134Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00834 AC: 2082AN: 249534Hom.: 19 AF XY: 0.00830 AC XY: 1124AN XY: 135378
GnomAD4 exome AF: 0.00883 AC: 12909AN: 1461770Hom.: 77 Cov.: 30 AF XY: 0.00882 AC XY: 6414AN XY: 727190
GnomAD4 genome AF: 0.00639 AC: 973AN: 152252Hom.: 6 Cov.: 32 AF XY: 0.00612 AC XY: 456AN XY: 74452
ClinVar
Submissions by phenotype
Netherton syndrome Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at