10-72097364-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001198800.3(ASCC1):c.1044C>T(p.Tyr348Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,613,400 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 Benign (★).
Frequency
Genomes: 𝑓 0.00097 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 2 hom. )
Consequence
ASCC1
NM_001198800.3 synonymous
NM_001198800.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.42
Genes affected
ASCC1 (HGNC:24268): (activating signal cointegrator 1 complex subunit 1) This gene encodes a subunit of the activating signal cointegrator 1 (ASC-1) complex. The ASC-1 complex is a transcriptional coactivator that plays an important role in gene transactivation by multiple transcription factors including activating protein 1 (AP-1), nuclear factor kappa-B (NF-kB) and serum response factor (SRF). The encoded protein contains an N-terminal KH-type RNA-binding motif which is required for AP-1 transactivation by the ASC-1 complex. Mutations in this gene are associated with Barrett esophagus and esophageal adenocarcinoma. Alternatively spliced transcripts encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 10-72097364-G-A is Benign according to our data. Variant chr10-72097364-G-A is described in ClinVar as [Benign]. Clinvar id is 720317.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.41 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000972 (148/152332) while in subpopulation AFR AF= 0.0031 (129/41572). AF 95% confidence interval is 0.00267. There are 0 homozygotes in gnomad4. There are 59 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 148 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASCC1 | NM_001198800.3 | c.1044C>T | p.Tyr348Tyr | synonymous_variant | Exon 10 of 10 | ENST00000672957.1 | NP_001185729.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000939 AC: 143AN: 152214Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000421 AC: 106AN: 251486Hom.: 1 AF XY: 0.000405 AC XY: 55AN XY: 135920
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GnomAD4 exome AF: 0.000155 AC: 226AN: 1461068Hom.: 2 Cov.: 30 AF XY: 0.000144 AC XY: 105AN XY: 726866
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GnomAD4 genome AF: 0.000972 AC: 148AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at