rs11983798

Positions:

• chr7-105640741-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATXN7L1	NM_020725.2	c.863-1172C>T		intron_variant		ENST00000419735.8
ATXN7L1	NM_001318229.2	c.215-1172C>T		intron_variant
ATXN7L1	NM_001385596.1	c.863-1172C>T		intron_variant
ATXN7L1	NM_138495.2	c.491-1172C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7L1	ENST00000419735.8	c.863-1172C>T		intron_variant		1	NM_020725.2	P1

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

Gnomad4 AFR AF: 0.0986

Gnomad4 AMR AF: 0.0571

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0772

Alfa AF: 0.0677 Hom.: 122

Bravo AF: 0.0708

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.67

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: rs11983798; hg19: chr7-105281188;