chr4-73740727-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_000584.4(CXCL8):c.64+5G>C variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,612,144 control chromosomes in the GnomAD database, including 1 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 Likely benign (★).
Frequency
Consequence
NM_000584.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL8 | NM_000584.4 | c.64+5G>C | splice_donor_5th_base_variant, intron_variant | ENST00000307407.8 | |||
CXCL8 | NM_001354840.3 | c.64+5G>C | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL8 | ENST00000307407.8 | c.64+5G>C | splice_donor_5th_base_variant, intron_variant | 1 | NM_000584.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000605 AC: 92AN: 152178Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000197 AC: 49AN: 249312Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134846
GnomAD4 exome AF: 0.0000507 AC: 74AN: 1459848Hom.: 0 Cov.: 29 AF XY: 0.0000399 AC XY: 29AN XY: 726290
GnomAD4 genome ? AF: 0.000637 AC: 97AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at