rs9303601

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184071.1(ATXN7L3-AS1):​n.91+2543A>G variant causes a intron, non coding transcript 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 NR_184071.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ATXN7L3-AS1	NR_184071.1	n.91+2543A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7L3-AS1	ENST00000586560.1	n.53+2539A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.898

Alfa AF: 0.870 Hom.: 30540

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9303601; hg19: chr17-42278841;