chr12-111634620-A-G

Variant names:

• chr12-111634620-A-G
• rs11065987
• ENST00000726948.1:n.110-14560A>G

Variant summary

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

The ENST00000726948.1(ATXN2-AS):​n.110-14560A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,942 control chromosomes in the GnomAD database, including 8,687 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 0.29 (8687 hom., cov: 30)
• Consequence: ATXN2-AS ENST00000726948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 186 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN2-AS	ENST00000726948.1	n.110-14560A>G		intron_variant	Intron 1 of 2
ATXN2-AS	ENST00000726949.1	n.548-14560A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43684 AN: 151822 Hom.: 8691 Cov.: 30

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.287 AC: 43665 AN: 151942 Hom.: 8687 Cov.: 30 AF XY: 0.279 AC XY: 20691 AN XY: 74264

African (AFR) AF: 0.0705 AC: 2927 AN: 41502

American (AMR) AF: 0.263 AC: 3996 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2241 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5168

South Asian (SAS) AF: 0.0767 AC: 370 AN: 4824

European-Finnish (FIN) AF: 0.379 AC: 3990 AN: 10540

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 29001 AN: 67928

Other (OTH) AF: 0.318 AC: 670 AN: 2110

Alfa AF: 0.382 Hom.: 42748

Bravo AF: 0.275

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11065987; hg19: chr12-112072424;