rs1544396

Variant names:

• chr12-111625071-T-C
• rs1544396
• ENST00000726948.1:n.110-24109T>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.110-24109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,932 control chromosomes in the GnomAD database, including 6,795 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 (6795 hom., cov: 30)
• Consequence: ATXN2-AS ENST00000726948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 27 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=-0.99).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN2-AS	ENST00000726948.1		n.110-24109T>C		intron	N/A
	ATXN2-AS	ENST00000726949.1		n.548-24109T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39504 AN: 151814 Hom.: 6800 Cov.: 30

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.260 AC: 39539 AN: 151932 Hom.: 6795 Cov.: 30 AF XY: 0.264 AC XY: 19637 AN XY: 74258

African (AFR) AF: 0.343 AC: 14201 AN: 41406

American (AMR) AF: 0.293 AC: 4455 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4601 AN: 5166

South Asian (SAS) AF: 0.320 AC: 1538 AN: 4804

European-Finnish (FIN) AF: 0.167 AC: 1764 AN: 10588

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

European-Non Finnish (NFE) AF: 0.174 AC: 11817 AN: 67966

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.209 Hom.: 12710

Bravo AF: 0.279

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.11
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1544396; hg19: chr12-112062875;