chr10-72102424-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP3BP6_ModerateBS1BS2
The NM_001198800.3(ASCC1):c.958-4974A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000556 in 1,547,816 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00031 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
ASCC1
NM_001198800.3 intron
NM_001198800.3 intron
Scores
2
Splicing: ADA: 0.9913
2
Clinical Significance
Conservation
PhyloP100: -0.565
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 -9 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
BP6
?
Variant 10-72102424-T-C is Benign according to our data. Variant chr10-72102424-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1896211.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000309 (47/152242) while in subpopulation AFR AF= 0.00111 (46/41488). AF 95% confidence interval is 0.000854. There are 1 homozygotes in gnomad4. There are 25 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 40 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASCC1 | NM_001198800.3 | c.958-4974A>G | intron_variant | ENST00000672957.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASCC1 | ENST00000672957.1 | c.958-4974A>G | intron_variant | NM_001198800.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152124Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000663 AC: 10AN: 150828Hom.: 0 AF XY: 0.0000494 AC XY: 4AN XY: 80894
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GnomAD4 exome AF: 0.0000279 AC: 39AN: 1395574Hom.: 0 Cov.: 29 AF XY: 0.0000232 AC XY: 16AN XY: 688494
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GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152242Hom.: 1 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74460
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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 | Aug 17, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at