16-89291038-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_013275.6(ANKRD11):c.372G>A(p.Thr124Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00217 in 1,612,538 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_013275.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD11 | NM_013275.6 | c.372G>A | p.Thr124Thr | synonymous_variant | Exon 5 of 13 | ENST00000301030.10 | NP_037407.4 | |
ANKRD11 | NM_001256182.2 | c.372G>A | p.Thr124Thr | synonymous_variant | Exon 6 of 14 | NP_001243111.1 | ||
ANKRD11 | NM_001256183.2 | c.372G>A | p.Thr124Thr | synonymous_variant | Exon 5 of 13 | NP_001243112.1 | ||
ANKRD11 | NR_045839.2 | n.1203G>A | non_coding_transcript_exon_variant | Exon 7 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0117 AC: 1779AN: 152116Hom.: 40 Cov.: 32
GnomAD3 exomes AF: 0.00294 AC: 731AN: 248664Hom.: 9 AF XY: 0.00216 AC XY: 292AN XY: 134952
GnomAD4 exome AF: 0.00117 AC: 1712AN: 1460304Hom.: 30 Cov.: 33 AF XY: 0.00101 AC XY: 737AN XY: 726500
GnomAD4 genome AF: 0.0117 AC: 1782AN: 152234Hom.: 40 Cov.: 32 AF XY: 0.0117 AC XY: 868AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:3
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KBG syndrome Benign:2
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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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at