rs9932707

Variant names:

• chr16-71828230-A-C
• rs9932707
• ENST00000683775.1:c.-180+19028A>C

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATXN1L	ENST00000683775.1	c.-180+19028A>C		intron_variant	Intron 1 of 2			ENSP00000507897.1

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;