12-111627093-T-C

Variant names:

• chr12-111627093-T-C
• rs9300319
• ENST00000726948.1:n.110-22087T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000726948.1(ATXN2-AS):​n.110-22087T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,956 control chromosomes in the GnomAD database, including 14,325 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 0.36 (14325 hom., cov: 31)
• Consequence: ATXN2-AS ENST00000726948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 12 publications found

Genes affected

ATXN2-AS (HGNC:51838): (ATXN2 antisense RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726948.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN2-AS	ENST00000726948.1		n.110-22087T>C		intron	N/A
	ATXN2-AS	ENST00000726949.1		n.548-22087T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54436 AN: 151840 Hom.: 14285 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.359 AC: 54538 AN: 151956 Hom.: 14325 Cov.: 31 AF XY: 0.360 AC XY: 26710 AN XY: 74288

African (AFR) AF: 0.684 AC: 28340 AN: 41418

American (AMR) AF: 0.330 AC: 5027 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4599 AN: 5164

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4806

European-Finnish (FIN) AF: 0.167 AC: 1762 AN: 10574

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11913 AN: 67962

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.275 Hom.: 1311

Bravo AF: 0.392

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.76
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9300319; hg19: chr12-112064897;