rs513150

Positions:

• chr7-69710667-G-A
• chr7-69710667-G-C
• chr7-69710667-G-T

Variant summary

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

The NM_015570.4(AUTS2):​c.309+110705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,102 control chromosomes in the GnomAD database, including 29,000 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 0.61 (29000 hom., cov: 33)
• Consequence: AUTS2 NM_015570.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AUTS2	NM_015570.4	c.309+110705G>A		intron_variant		ENST00000342771.10	NP_056385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AUTS2	ENST00000342771.10	c.309+110705G>A		intron_variant		1	NM_015570.4	ENSP00000344087	P4

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93374 AN: 151984 Hom.: 28984 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.614 AC: 93422 AN: 152102 Hom.: 29000 Cov.: 33 AF XY: 0.612 AC XY: 45508 AN XY: 74338

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.614

Alfa AF: 0.625 Hom.: 4625

Bravo AF: 0.610

Asia WGS AF: 0.632 AC: 2198 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.78

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: rs513150; hg19: chr7-69175653;