7-105808899-A-G

Variant names:

• chr7-105808899-A-G
• rs996642
• NM_020725.2:c.251-20191T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020725.2(ATXN7L1):​c.251-20191T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,282 control chromosomes in the GnomAD database, including 51,718 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 0.82 (51718 hom., cov: 34)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	NM_020725.2	MANE Select	c.251-20191T>C		intron	N/A	NP_065776.1
	ATXN7L1	NM_001385596.1		c.251-20191T>C		intron	N/A	NP_001372525.1
	ATXN7L1	NM_152749.3		c.251-20191T>C		intron	N/A	NP_689962.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	ENST00000419735.8	TSL:1 MANE Select	c.251-20191T>C		intron	N/A	ENSP00000410759.3
	ATXN7L1	ENST00000318724.8	TSL:1	c.251-20191T>C		intron	N/A	ENSP00000326344.4
	ATXN7L1	ENST00000478915.1	TSL:3	c.98-20191T>C		intron	N/A	ENSP00000418679.1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124903 AN: 152164 Hom.: 51666 Cov.: 34

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.821 AC: 125015 AN: 152282 Hom.: 51718 Cov.: 34 AF XY: 0.819 AC XY: 60967 AN XY: 74442

African (AFR) AF: 0.903 AC: 37534 AN: 41566

American (AMR) AF: 0.842 AC: 12881 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2783 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5097 AN: 5192

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.721 AC: 7638 AN: 10592

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52555 AN: 68014

Other (OTH) AF: 0.833 AC: 1762 AN: 2116

Alfa AF: 0.787 Hom.: 80329

Bravo AF: 0.835

Asia WGS AF: 0.881 AC: 3063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	10
DANN	Benign	0.31
PhyloP100		1.2
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: rs996642; hg19: chr7-105449345;