chr3-63956021-T-G

Position:

• chr3-63956021-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001377405.1(ATXN7):​c.499+3538T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,252 control chromosomes in the GnomAD database, including 1,061 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 0.11 (1061 hom., cov: 31)
• Consequence: ATXN7 NM_001377405.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62

Genes affected

ATXN7 (HGNC:10560): (ataxin 7) The autosomal dominant cerebellar ataxias (ADCA) are a heterogeneous group of neurodegenerative disorders characterized by progressive degeneration of the cerebellum, brain stem and spinal cord. Clinically, ADCA has been divided into three groups: ADCA types I-III. ADCAI is genetically heterogeneous, with five genetic loci, designated spinocerebellar ataxia (SCA) 1, 2, 3, 4 and 6, being assigned to five different chromosomes. ADCAII, which always presents with retinal degeneration (SCA7), and ADCAIII often referred to as the 'pure' cerebellar syndrome (SCA5), are most likely homogeneous disorders. Several SCA genes have been cloned and shown to contain CAG repeats in their coding regions. ADCA is caused by the expansion of the CAG repeats, producing an elongated polyglutamine tract in the corresponding protein. The expanded repeats are variable in size and unstable, usually increasing in size when transmitted to successive generations. This locus has been mapped to chromosome 3, and it has been determined that the diseased allele associated with spinocerebellar ataxia-7 contains 37-306 CAG repeats (near the N-terminus), compared to 4-35 in the normal allele. The encoded protein is a component of the SPT3/TAF9/GCN5 acetyltransferase (STAGA) and TBP-free TAF-containing (TFTC) chromatin remodeling complexes, and it thus plays a role in transcriptional regulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATXN7	NM_001377405.1	c.499+3538T>G		intron_variant		ENST00000674280.1
ATXN7	NM_000333.4	c.499+3538T>G		intron_variant
ATXN7	NM_001177387.1	c.499+3538T>G		intron_variant
ATXN7	NM_001377406.1	c.499+3538T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATXN7	ENST00000674280.1	c.499+3538T>G		intron_variant			NM_001377405.1	P2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16354 AN: 152134 Hom.: 1060 Cov.: 31

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.107 AC: 16360 AN: 152252 Hom.: 1061 Cov.: 31 AF XY: 0.106 AC XY: 7859 AN XY: 74430

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.133

Alfa AF: 0.132 Hom.: 831

Bravo AF: 0.115

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.023
DANN	Benign	0.42

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: rs3821902; hg19: chr3-63941697;