ENST00000726948.1:n.109+7494G>C

Variant names:

• chr12-111606529-G-C
• rs3809274
• ENST00000726948.1:n.109+7494G>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.109+7494G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,980 control chromosomes in the GnomAD database, including 6,578 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 0.26 (6578 hom., cov: 31)
• Consequence: ATXN2-AS ENST00000726948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 14 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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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.109+7494G>C		intron	N/A
	ATXN2-AS	ENST00000726949.1		n.547+6364G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38911 AN: 151862 Hom.: 6583 Cov.: 31

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.256 AC: 38945 AN: 151980 Hom.: 6578 Cov.: 31 AF XY: 0.261 AC XY: 19379 AN XY: 74274

African (AFR) AF: 0.328 AC: 13614 AN: 41450

American (AMR) AF: 0.290 AC: 4410 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3466

East Asian (EAS) AF: 0.891 AC: 4612 AN: 5176

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4810

European-Finnish (FIN) AF: 0.167 AC: 1767 AN: 10558

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11826 AN: 67978

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.217 Hom.: 521

Bravo AF: 0.275

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.7
DANN	Benign	0.51
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs3809274; hg19: chr12-112044333;