chrX-75053593-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001271696.3(ABCB7):c.2044-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000571 in 1,173,332 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. 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_001271696.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB7 | NM_001271696.3 | c.2044-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000373394.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB7 | ENST00000373394.8 | c.2044-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001271696.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112421Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34601
GnomAD3 exomes AF: 0.00000789 AC: 1AN: 126691Hom.: 0 AF XY: 0.0000240 AC XY: 1AN XY: 41589
GnomAD4 exome AF: 0.0000613 AC: 65AN: 1060911Hom.: 0 Cov.: 30 AF XY: 0.0000610 AC XY: 21AN XY: 344485
GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112421Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34601
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at