1-109488566-T-G

Variant summary

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

The NM_001350175.2(ATXN7L2):c.879+101T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,356,094 control chromosomes in the GnomAD database, including 17,802 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 0.13 (1640 hom., cov: 33)
  • Exomes 𝑓: 0.16 (16162 hom.)
• Consequence: ATXN7L2 NM_001350175.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

ATXN7L2 (HGNC:28713): (ataxin 7 like 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATXN7L2	NM_001350175.2	c.879+101T>G		intron_variant		ENST00000683729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7L2	ENST00000683729.1	c.879+101T>G		intron_variant			NM_001350175.2	P2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19706 AN: 152084 Hom.: 1642 Cov.: 33

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.158 AC: 190608 AN: 1203892 Hom.: 16162 AF XY: 0.159 AC XY: 95143 AN XY: 597196

Gnomad4 AFR exome AF: 0.0306

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.205

Gnomad4 EAS exome AF: 0.299

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.170

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.163

GnomAD4 genome AF: 0.129 AC: 19709 AN: 152202 Hom.: 1640 Cov.: 33 AF XY: 0.132 AC XY: 9796 AN XY: 74406

Gnomad4 AFR AF: 0.0347

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.158

Alfa AF: 0.156 Hom.: 3510

Bravo AF: 0.126

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.7
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12049330; hg19: chr1-110031188; COSMIC: COSV63992608; COSMIC: COSV63992608;