7-105633011-C-T

Variant names:

• chr7-105633011-C-T
• rs1615197
• NM_020725.2:c.1202+5342G>A

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+5342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 149,752 control chromosomes in the GnomAD database, including 31,893 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 0.65 (31893 hom., cov: 26)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020725.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	NM_020725.2	MANE Select	c.1202+5342G>A		intron	N/A	NP_065776.1	Q9ULK2-1
	ATXN7L1	NM_001385596.1		c.1202+5342G>A		intron	N/A	NP_001372525.1
	ATXN7L1	NM_138495.2		c.830+5342G>A		intron	N/A	NP_612504.1	Q9ULK2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	ENST00000419735.8	TSL:1 MANE Select	c.1202+5342G>A		intron	N/A	ENSP00000410759.3	Q9ULK2-1
	ATXN7L1	ENST00000474433.5	TSL:1	n.*777+5342G>A		intron	N/A	ENSP00000420483.1	F8WDE7
	ATXN7L1	ENST00000472195.1	TSL:5	c.830+5342G>A		intron	N/A	ENSP00000419566.1	C9K0V9

Frequencies

GnomAD3 genomes AF: 0.652 AC: 97514 AN: 149640 Hom.: 31850 Cov.: 26

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.652 AC: 97623 AN: 149752 Hom.: 31893 Cov.: 26 AF XY: 0.657 AC XY: 47905 AN XY: 72904

African (AFR) AF: 0.710 AC: 28927 AN: 40728

American (AMR) AF: 0.697 AC: 10509 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2153 AN: 3462

East Asian (EAS) AF: 0.804 AC: 4127 AN: 5134

South Asian (SAS) AF: 0.716 AC: 3406 AN: 4754

European-Finnish (FIN) AF: 0.658 AC: 6437 AN: 9782

Middle Eastern (MID) AF: 0.568 AC: 159 AN: 280

European-Non Finnish (NFE) AF: 0.593 AC: 40060 AN: 67558

Other (OTH) AF: 0.649 AC: 1345 AN: 2074

Alfa AF: 0.612 Hom.: 91235

Bravo AF: 0.657

Asia WGS AF: 0.771 AC: 2676 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.46
PhyloP100		-1.9
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: rs1615197; hg19: chr7-105273458;