7-27095697-ATGGTGGTGG-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_005522.5(HOXA1):c.207_215delCCACCACCA(p.His70_His72del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00329 in 949,682 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005522.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HOXA1 | NM_005522.5 | c.207_215delCCACCACCA | p.His70_His72del | disruptive_inframe_deletion | Exon 1 of 2 | ENST00000643460.2 | NP_005513.2 | |
HOXA1 | NM_153620.3 | c.207_215delCCACCACCA | p.His70_His72del | disruptive_inframe_deletion | Exon 1 of 3 | NP_705873.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXA1 | ENST00000643460.2 | c.207_215delCCACCACCA | p.His70_His72del | disruptive_inframe_deletion | Exon 1 of 2 | NM_005522.5 | ENSP00000494260.2 | |||
HOXA1 | ENST00000355633.5 | c.207_215delCCACCACCA | p.His70_His72del | disruptive_inframe_deletion | Exon 1 of 3 | 1 | ENSP00000347851.5 | |||
HOTAIRM1 | ENST00000495032.1 | n.26+41_26+49delTGGTGGTGG | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00184 AC: 260AN: 141482Hom.: 3 Cov.: 30
GnomAD3 exomes AF: 0.00364 AC: 846AN: 232380Hom.: 11 AF XY: 0.00408 AC XY: 513AN XY: 125726
GnomAD4 exome AF: 0.00354 AC: 2864AN: 808074Hom.: 22 AF XY: 0.00427 AC XY: 1658AN XY: 388582
GnomAD4 genome AF: 0.00183 AC: 259AN: 141608Hom.: 3 Cov.: 30 AF XY: 0.00223 AC XY: 154AN XY: 69194
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at