Variant chr10-72102274-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001198800.3(ASCC1):c.958-4824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,437,430 control chromosomes in the GnomAD database, including 124,738 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 10031 hom., cov: 32)

Exomes 𝑓: 0.42 ( 114707 hom. )

Consequence

ASCC1
NM_001198800.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.137

Variant links:

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]

ASCC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 10-72102274-C-T is Benign according to our data. Variant chr10-72102274-C-T is described in ClinVar as [Benign]. Clinvar id is 1289137.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASCC1	NM_001198800.3 linkuse as main transcript	c.958-4824G>A		intron_variant		ENST00000672957.1	NP_001185729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASCC1	ENST00000672957.1 linkuse as main transcript	c.958-4824G>A		intron_variant			NM_001198800.3	ENSP00000500935	P1	Q8N9N2-2

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52831

AN:

151854

Hom.:

10030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.484

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.417

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.433

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.381

GnomAD4 exome

AF:

0.417

AC:

535680

AN:

1285458

Hom.:

114707

AF XY:

0.420

AC XY:

268492

AN XY:

639380

show subpopulations

Gnomad4 AFR exome

AF:

0.208

Gnomad4 AMR exome

AF:

0.341

Gnomad4 ASJ exome

AF:

0.425

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.450

Gnomad4 FIN exome

AF:

0.357

Gnomad4 NFE exome

AF:

0.435

Gnomad4 OTH exome

AF:

0.402

GnomAD4 genome

AF:

0.348

AC:

52839

AN:

151972

Hom.:

10031

Cov.:

AF XY:

0.342

AC XY:

25430

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.356

Gnomad4 ASJ

AF:

0.417

Gnomad4 EAS

AF:

0.136

Gnomad4 SAS

AF:

0.434

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.433

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.411

Hom.:

19743

Bravo

AF:

0.341

Asia WGS

AF:

0.236

AC:

820

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

6.9

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over