rs9373571

Positions:

• chr6-100685958-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006828.4(ASCC3):​c.2152-6206A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,044 control chromosomes in the GnomAD database, including 10,860 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (10860 hom., cov: 32)
• Consequence: ASCC3 NM_006828.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

Genes affected

ASCC3 (HGNC:18697): (activating signal cointegrator 1 complex subunit 3) This gene encodes a protein that belongs to a family of helicases that are involved in the ATP-dependent unwinding of nucleic acid duplexes. The encoded protein is the largest subunit of the activating signal cointegrator 1 complex that is involved in DNA repair and resistance to alkylation damage. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASCC3	NM_006828.4	c.2152-6206A>T		intron_variant		ENST00000369162.7	NP_006819.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASCC3	ENST00000369162.7	c.2152-6206A>T		intron_variant		5	NM_006828.4	ENSP00000358159	P1
ASCC3	ENST00000324696.8	c.*1854-6206A>T		intron_variant, NMD_transcript_variant		2		ENSP00000320252

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52864 AN: 151926 Hom.: 10855 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.389

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.348 AC: 52883 AN: 152044 Hom.: 10860 Cov.: 32 AF XY: 0.344 AC XY: 25583 AN XY: 74300

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.394

Alfa AF: 0.391 Hom.: 1555

Bravo AF: 0.342

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs9373571; hg19: chr6-101133834;