rs9303601

Variant names:

• chr17-44201473-A-G
• rs9303601
• ENST00000586560.1:n.53+2539A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-44201473-A-G
• chr17-44201473-A-T

Variant summary

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

The ENST00000586560.1(ATXN7L3-AS1):​n.53+2539A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,330 control chromosomes in the GnomAD database, including 61,828 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 0.90 (61828 hom., cov: 34)
• Consequence: ATXN7L3-AS1 ENST00000586560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 9 publications found

Genes affected

ATXN7L3-AS1 (HGNC:55298): (ATXN7L3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATXN7L3-AS1	NR_184071.1	n.91+2543A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN7L3-AS1	ENST00000586560.1	n.53+2539A>G		intron_variant	Intron 1 of 1	3
ATXN7L3-AS1	ENST00000717216.1	n.139+2543A>G		intron_variant	Intron 1 of 1
ATXN7L3-AS1	ENST00000848873.1	n.90+2543A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136871 AN: 152212 Hom.: 61767 Cov.: 34

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.899 AC: 136989 AN: 152330 Hom.: 61828 Cov.: 34 AF XY: 0.898 AC XY: 66838 AN XY: 74468

African (AFR) AF: 0.974 AC: 40491 AN: 41588

American (AMR) AF: 0.886 AC: 13567 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3103 AN: 3472

East Asian (EAS) AF: 0.980 AC: 5084 AN: 5188

South Asian (SAS) AF: 0.872 AC: 4214 AN: 4832

European-Finnish (FIN) AF: 0.856 AC: 9080 AN: 10604

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58485 AN: 68022

Other (OTH) AF: 0.898 AC: 1901 AN: 2116

Alfa AF: 0.871 Hom.: 33494

Bravo AF: 0.910

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9303601; hg19: chr17-42278841;