rs9932707

Positions:

• chr16-71828230-A-C
• chr16-71828230-A-G
• chr16-71828230-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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]

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 (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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN1L	ENST00000683775.1	c.-180+19028A>C		intron_variant				ENSP00000507897	P1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71651 AN: 151894 Hom.: 18099 Cov.: 32

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.: 32 AF XY: 0.482 AC XY: 35852 AN XY: 74310

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

Other links and lift over

dbSNP: rs9932707; hg19: chr16-71862133;