Variant rs9932707 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000683775.1(ATXN1L):c.-180+19028A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,012 control chromosomes in the GnomAD database, including 18,111 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 0.47 ( 18111 hom., cov: 32)

Consequence

ATXN1L
ENST00000683775.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

Variant links:

Genes affected

ATXN1L (HGNC:33279): (ataxin 1 like) Predicted to enable DNA binding activity and RNA binding activity. Predicted to be involved in several processes, including learning or memory; regulation of transcription, DNA-templated; and social behavior. Predicted to act upstream of or within several processes, including lung alveolus development; negative regulation of transcription by RNA polymerase II; and positive regulation of hematopoietic stem cell proliferation. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ATXN1L links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.71828230A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN1L	ENST00000683775.1 linkuse as main transcript	c.-180+19028A>C		intron_variant				ENSP00000507897.1		P0C7T5

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71651

AN:

151894

Hom.:

18099

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.590

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.919

Gnomad SAS

AF:

0.691

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.464

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

GnomAD4 genome

AF:

0.472

AC:

71680

AN:

152012

Hom.:

18111

Cov.:

AF XY:

0.482

AC XY:

35852

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.591

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.919

Gnomad4 SAS

AF:

0.690

Gnomad4 FIN

AF:

0.552

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.467

Alfa

AF:

0.456

Hom.:

20519

Bravo

AF:

0.471

Asia WGS

AF:

0.765

AC:

2657

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

1.5

DANN

Benign

0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over