rs10242311

Positions:

• chr7-105633273-A-C

Variant summary

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

The NM_020725.2(ATXN7L1):​c.1202+5080T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 152,302 control chromosomes in the GnomAD database, including 491 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 0.065 (491 hom., cov: 33)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

ATXN7L1 (HGNC:22210): (ataxin 7 like 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN7L1	NM_020725.2	c.1202+5080T>G		intron_variant		ENST00000419735.8	NP_065776.1
ATXN7L1	NM_001318229.2	c.554+5080T>G		intron_variant			NP_001305158.1
ATXN7L1	NM_001385596.1	c.1202+5080T>G		intron_variant			NP_001372525.1
ATXN7L1	NM_138495.2	c.830+5080T>G		intron_variant			NP_612504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.1202+5080T>G		intron_variant		1	NM_020725.2	ENSP00000410759	P1

Frequencies

GnomAD3 genomes AF: 0.0653 AC: 9935 AN: 152184 Hom.: 490 Cov.: 33

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0653 AC: 9944 AN: 152302 Hom.: 491 Cov.: 33 AF XY: 0.0668 AC XY: 4975 AN XY: 74464

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0500

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0680 Hom.: 508

Bravo AF: 0.0648

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs10242311; hg19: chr7-105273720;