chr18-74260915-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_148923.4(CYB5A):c.288G>A(p.Pro96=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,608,572 control chromosomes in the GnomAD database, including 21,414 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_148923.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYB5A | NM_148923.4 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/5 | ENST00000340533.9 | |
CYB5A | NM_001914.4 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/6 | ||
CYB5A | XM_011525835.3 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/4 | ||
CYB5A | NM_001190807.3 | c.258+2434G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYB5A | ENST00000340533.9 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/5 | 1 | NM_148923.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23288AN: 151978Hom.: 1856 Cov.: 33
GnomAD3 exomes AF: 0.157 AC: 39337AN: 251228Hom.: 3464 AF XY: 0.152 AC XY: 20690AN XY: 135778
GnomAD4 exome AF: 0.160 AC: 232796AN: 1456476Hom.: 19551 Cov.: 29 AF XY: 0.158 AC XY: 114687AN XY: 724832
GnomAD4 genome ? AF: 0.153 AC: 23311AN: 152096Hom.: 1863 Cov.: 33 AF XY: 0.154 AC XY: 11414AN XY: 74340
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at