chr7-105633273-A-C

Variant names:

• chr7-105633273-A-C
• rs10242311
• NM_020725.2:c.1202+5080T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ENSG00000295921 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATXN7L1	NM_020725.2	c.1202+5080T>G		intron_variant	Intron 7 of 11	ENST00000419735.8	NP_065776.1
ATXN7L1	NM_001385596.1	c.1202+5080T>G		intron_variant	Intron 7 of 11		NP_001372525.1
ATXN7L1	NM_138495.2	c.830+5080T>G		intron_variant	Intron 5 of 9		NP_612504.1
ATXN7L1	NM_001318229.2	c.554+5080T>G		intron_variant	Intron 7 of 9		NP_001305158.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.1202+5080T>G		intron_variant	Intron 7 of 11	1	NM_020725.2	ENSP00000410759.3

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

African (AFR) AF: 0.0354 AC: 1470 AN: 41580

American (AMR) AF: 0.0673 AC: 1030 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1281 AN: 5176

South Asian (SAS) AF: 0.151 AC: 726 AN: 4814

European-Finnish (FIN) AF: 0.0500 AC: 531 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0645 AC: 4387 AN: 68028

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0652 Hom.: 701

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
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10242311; hg19: chr7-105273720;