rs734930

Positions:

• chr7-70555174-T-C

Variant summary

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

The NM_015570.4(AUTS2):​c.690+119393T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,012 control chromosomes in the GnomAD database, including 21,652 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 0.53 (21652 hom., cov: 32)
• Consequence: AUTS2 NM_015570.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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]

LOC124901669 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AUTS2	NM_015570.4	c.690+119393T>C		intron_variant		ENST00000342771.10
LOC124901669	XR_007060376.1	n.7646T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AUTS2	ENST00000342771.10	c.690+119393T>C		intron_variant		1	NM_015570.4	P4
AUTS2	ENST00000406775.6	c.690+119393T>C		intron_variant		1
AUTS2	ENST00000644939.1	c.690+119393T>C		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79896 AN: 151894 Hom.: 21623 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.526 AC: 79979 AN: 152012 Hom.: 21652 Cov.: 32 AF XY: 0.530 AC XY: 39399 AN XY: 74286

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.545

Alfa AF: 0.544 Hom.: 47054

Bravo AF: 0.520

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.72
DANN	Benign	0.69

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: rs734930; hg19: chr7-70020160;