rs11983798

Variant names:

• chr7-105640741-G-A
• rs11983798
• NM_020725.2:c.863-1172C>T

Variant summary

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

The NM_020725.2(ATXN7L1):​c.863-1172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0744 in 152,252 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 0.074 (491 hom., cov: 32)
• Consequence: ATXN7L1 NM_020725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0961 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.863-1172C>T		intron	N/A	NP_065776.1
	ATXN7L1	NM_001385596.1		c.863-1172C>T		intron	N/A	NP_001372525.1
	ATXN7L1	NM_138495.2		c.491-1172C>T		intron	N/A	NP_612504.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7L1	ENST00000419735.8	TSL:1 MANE Select	c.863-1172C>T		intron	N/A	ENSP00000410759.3
	ATXN7L1	ENST00000474433.5	TSL:1	n.*438-1172C>T		intron	N/A	ENSP00000420483.1
	ATXN7L1	ENST00000472195.1	TSL:5	c.491-1172C>T		intron	N/A	ENSP00000419566.1

Frequencies

GnomAD3 genomes AF: 0.0745 AC: 11335 AN: 152134 Hom.: 493 Cov.: 32

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0744 AC: 11324 AN: 152252 Hom.: 491 Cov.: 32 AF XY: 0.0760 AC XY: 5655 AN XY: 74456

African (AFR) AF: 0.0986 AC: 4096 AN: 41542

American (AMR) AF: 0.0571 AC: 874 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5174

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4824

European-Finnish (FIN) AF: 0.0939 AC: 996 AN: 10604

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4308 AN: 68022

Other (OTH) AF: 0.0772 AC: 163 AN: 2112

Alfa AF: 0.0654 Hom.: 738

Bravo AF: 0.0708

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.67
PhyloP100		0.53
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: rs11983798; hg19: chr7-105281188;