10-90915892-GAA-GA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_014391.3(ANKRD1):c.652-13delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,611,048 control chromosomes in the GnomAD database, including 20,419 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014391.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD1 | NM_014391.3 | c.652-13delT | intron_variant | Intron 6 of 8 | ENST00000371697.4 | NP_055206.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.173 AC: 26111AN: 151198Hom.: 2326 Cov.: 25
GnomAD3 exomes AF: 0.150 AC: 37486AN: 249262Hom.: 2910 AF XY: 0.151 AC XY: 20297AN XY: 134794
GnomAD4 exome AF: 0.155 AC: 226340AN: 1459732Hom.: 18087 Cov.: 30 AF XY: 0.155 AC XY: 112313AN XY: 726162
GnomAD4 genome AF: 0.173 AC: 26145AN: 151316Hom.: 2332 Cov.: 25 AF XY: 0.171 AC XY: 12627AN XY: 73900
ClinVar
Submissions by phenotype
not provided Benign:2
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Variant summary: The ANKRD1 c.652-13delT variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a benign outcome for this variant. 3/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 18376/112060 control chromosomes (1459 homozygotes) from ExAC at a frequency of 0.1639836, which is approximately 4770 times the estimated maximal expected allele frequency of a pathogenic ANKRD1 variant (0.0000344), thus it is a common benign polymorphism. This variant has also been reported as a polymorphism in the literature (Arimura_2009). In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely benign. Taken together, this variant is classified as benign. -
not specified Benign:1
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Dilated Cardiomyopathy, Dominant Benign:1
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ANKRD1-related dilated cardiomyopathy Benign:1
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Hypertrophic cardiomyopathy 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at