Variant chr10-72097226-A-G 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.*108T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 816,300 control chromosomes in the GnomAD database, including 91,140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 19382 hom., cov: 32)

Exomes 𝑓: 0.46 ( 71758 hom. )

Consequence

ASCC1
NM_001198800.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.103

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 10-72097226-A-G is Benign according to our data. Variant chr10-72097226-A-G is described in ClinVar as [Benign]. Clinvar id is 1262551.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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.*108T>C		3_prime_UTR_variant	10/10	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.*108T>C		3_prime_UTR_variant	10/10		NM_001198800.3	ENSP00000500935	P1	Q8N9N2-2

Frequencies

GnomAD3 genomes

AF:

0.495

AC:

75199

AN:

151920

Hom.:

19348

Cov.:

show subpopulations

Gnomad AFR

AF:

0.625

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.522

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.497

GnomAD3 exomes

AF:

0.453

AC:

112790

AN:

249026

Hom.:

26510

AF XY:

0.459

AC XY:

61862

AN XY:

134818

show subpopulations

Gnomad AFR exome

AF:

0.627

Gnomad AMR exome

AF:

0.379

Gnomad ASJ exome

AF:

0.418

Gnomad EAS exome

AF:

0.293

Gnomad SAS exome

AF:

0.535

Gnomad FIN exome

AF:

0.391

Gnomad NFE exome

AF:

0.468

Gnomad OTH exome

AF:

0.458

GnomAD4 exome

AF:

0.459

AC:

304663

AN:

664262

Hom.:

71758

Cov.:

AF XY:

0.465

AC XY:

166745

AN XY:

358822

show subpopulations

Gnomad4 AFR exome

AF:

0.622

Gnomad4 AMR exome

AF:

0.385

Gnomad4 ASJ exome

AF:

0.421

Gnomad4 EAS exome

AF:

0.302

Gnomad4 SAS exome

AF:

0.535

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.467

Gnomad4 OTH exome

AF:

0.468

GnomAD4 genome

AF:

0.495

AC:

75280

AN:

152038

Hom.:

19382

Cov.:

AF XY:

0.486

AC XY:

36155

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.625

Gnomad4 AMR

AF:

0.431

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.522

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.469

Gnomad4 OTH

AF:

0.496

Alfa

AF:

0.468

Hom.:

30316

Bravo

AF:

0.501

Asia WGS

AF:

0.438

AC:

1520

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

6.7

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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