chr6-34970052-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_015245.3(ANKS1A):c.321C>T(p.Asn107=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000422 in 1,614,134 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00058 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 1 hom. )
Consequence
ANKS1A
NM_015245.3 synonymous
NM_015245.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.780
Genes affected
ANKS1A (HGNC:20961): (ankyrin repeat and sterile alpha motif domain containing 1A) Predicted to enable ephrin receptor binding activity. Predicted to be involved in ephrin receptor signaling pathway; neuron remodeling; and substrate-dependent cell migration. Predicted to act upstream of or within negative regulation of ubiquitin-dependent protein catabolic process and regulation of ephrin receptor signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 6-34970052-C-T is Benign according to our data. Variant chr6-34970052-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 721533.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.78 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.321C>T | p.Asn107= | synonymous_variant | 3/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.321C>T | p.Asn107= | synonymous_variant | 3/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.321C>T | p.Asn107= | synonymous_variant | 3/25 | P1 | |||
ANKS1A | ENST00000650178.1 | c.321C>T | p.Asn107= | synonymous_variant | 3/10 |
Frequencies
GnomAD3 genomes ? AF: 0.000578 AC: 88AN: 152186Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000354 AC: 89AN: 251254Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135794
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GnomAD4 exome AF: 0.000406 AC: 593AN: 1461830Hom.: 1 Cov.: 30 AF XY: 0.000385 AC XY: 280AN XY: 727220
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GnomAD4 genome ? AF: 0.000578 AC: 88AN: 152304Hom.: 1 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2018 | - - |
Computational scores
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Benign
Cadd
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Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at