rs763931520
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_052997.3(ANKRD30A):c.3939_3940delTG(p.Glu1314ThrfsTer28) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00429 in 1,609,780 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0030 ( 2 hom., cov: 30)
Exomes 𝑓: 0.0044 ( 23 hom. )
Consequence
ANKRD30A
NM_052997.3 frameshift
NM_052997.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.06
Genes affected
ANKRD30A (HGNC:17234): (ankyrin repeat domain 30A) This gene encodes a DNA-binding transcription factor that is uniquely expressed in mammary epithelium and the testis. Altered expression levels have been associated with breast cancer progression. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD30A | ENST00000361713.2 | c.3939_3940delTG | p.Glu1314ThrfsTer28 | frameshift_variant | Exon 34 of 36 | 5 | NM_052997.3 | ENSP00000354432.2 | ||
ANKRD30A | ENST00000374660.7 | c.4296_4297delTG | p.Glu1433ThrfsTer28 | frameshift_variant | Exon 40 of 42 | 5 | ENSP00000363792.2 | |||
ANKRD30A | ENST00000602533.7 | c.3939_3940delTG | p.Glu1314ThrfsTer28 | frameshift_variant | Exon 34 of 36 | 5 | ENSP00000473551.2 | |||
ANKRD30A | ENST00000696674.1 | c.672_673delTG | p.Glu225ThrfsTer28 | frameshift_variant | Exon 1 of 2 | ENSP00000512798.1 |
Frequencies
GnomAD3 genomes AF: 0.00304 AC: 459AN: 150902Hom.: 2 Cov.: 30
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GnomAD3 exomes AF: 0.00264 AC: 653AN: 247458Hom.: 2 AF XY: 0.00270 AC XY: 362AN XY: 134322
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GnomAD4 exome AF: 0.00442 AC: 6444AN: 1458878Hom.: 23 AF XY: 0.00421 AC XY: 3058AN XY: 725754
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GnomAD4 genome AF: 0.00304 AC: 459AN: 150902Hom.: 2 Cov.: 30 AF XY: 0.00305 AC XY: 225AN XY: 73678
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Familial cancer of breast Uncertain:1
Uncertain significance, no assertion criteria provided | research | Faculty of Pharmacy, Medical University of Gdansk | Feb 01, 2014 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at