8-41653768-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000037.4(ANK1):c.*2022G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 152,310 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000037.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANK1 | ENST00000289734 | c.*2022G>A | 3_prime_UTR_variant | Exon 43 of 43 | 1 | NM_000037.4 | ENSP00000289734.8 | |||
ANK1 | ENST00000265709 | c.*1959G>A | 3_prime_UTR_variant | Exon 43 of 43 | 1 | ENSP00000265709.8 | ||||
ANK1 | ENST00000347528 | c.*1959G>A | 3_prime_UTR_variant | Exon 42 of 42 | 1 | ENSP00000339620.4 | ||||
ANK1 | ENST00000522543 | c.*1959G>A | 3_prime_UTR_variant | Exon 4 of 4 | 2 | ENSP00000430368.1 |
Frequencies
GnomAD3 genomes AF: 0.0196 AC: 2985AN: 152192Hom.: 84 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 82Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 68
GnomAD4 genome AF: 0.0196 AC: 2988AN: 152310Hom.: 85 Cov.: 33 AF XY: 0.0188 AC XY: 1400AN XY: 74474
ClinVar
Submissions by phenotype
Hereditary spherocytosis type 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
- -
Spherocytosis Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at