rs12698902

Positions:

• chr7-70372333-A-G

Variant summary

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

The NM_015570.4(AUTS2):​c.661-63419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,084 control chromosomes in the GnomAD database, including 9,195 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 0.33 (9195 hom., cov: 32)
• Consequence: AUTS2 NM_015570.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

AUTS2 (HGNC:14262): (activator of transcription and developmental regulator AUTS2) This gene has been implicated in neurodevelopment and as a candidate gene for numerous neurological disorders, including autism spectrum disorders, intellectual disability, and developmental delay. Mutations in this gene have also been associated with non-neurological disorders, such as acute lymphoblastic leukemia, aging of the skin, early-onset androgenetic alopecia, and certain cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AUTS2	NM_015570.4	c.661-63419A>G		intron_variant		ENST00000342771.10	NP_056385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AUTS2	ENST00000342771.10	c.661-63419A>G		intron_variant		1	NM_015570.4	ENSP00000344087	P4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50855 AN: 151966 Hom.: 9156 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.335 AC: 50945 AN: 152084 Hom.: 9195 Cov.: 32 AF XY: 0.338 AC XY: 25135 AN XY: 74338

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.304

Alfa AF: 0.287 Hom.: 13153

Bravo AF: 0.336

Asia WGS AF: 0.276 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.55

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: rs12698902; hg19: chr7-69837319;