rs7238987
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000340533.9(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
ENST00000340533.9 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYB5A | NM_148923.4 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/5 | ENST00000340533.9 | NP_683725.1 | |
CYB5A | NM_001914.4 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/6 | NP_001905.1 | ||
CYB5A | XM_011525835.3 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/4 | XP_011524137.1 | ||
CYB5A | NM_001190807.3 | c.258+2434G>A | intron_variant | NP_001177736.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYB5A | ENST00000340533.9 | c.288G>A | p.Pro96= | splice_region_variant, synonymous_variant | 3/5 | 1 | NM_148923.4 | ENSP00000341625 | 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:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at