7-69598914-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_015570.4(AUTS2):​c.-740T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 153,740 control chromosomes in the GnomAD database, including 5,668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 5600 hom., cov: 30)
Exomes 𝑓: 0.23 ( 68 hom. )

Consequence

AUTS2
NM_015570.4 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.158
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 7-69598914-T-G is Benign according to our data. Variant chr7-69598914-T-G is described in ClinVar as [Benign]. Clinvar id is 1226087.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AUTS2NM_015570.4 linkuse as main transcriptc.-740T>G 5_prime_UTR_variant 1/19 ENST00000342771.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AUTS2ENST00000342771.10 linkuse as main transcriptc.-740T>G 5_prime_UTR_variant 1/191 NM_015570.4 P4Q8WXX7-1
AUTS2ENST00000644939.1 linkuse as main transcriptc.-740T>G 5_prime_UTR_variant 1/19 A1
AUTS2ENST00000406775.6 linkuse as main transcript upstream_gene_variant 1 Q8WXX7-2

Frequencies

GnomAD3 genomes
AF:
0.253
AC:
38371
AN:
151680
Hom.:
5597
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.341
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.261
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.561
Gnomad SAS
AF:
0.341
Gnomad FIN
AF:
0.162
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.187
Gnomad OTH
AF:
0.227
GnomAD4 exome
AF:
0.228
AC:
443
AN:
1942
Hom.:
68
Cov.:
0
AF XY:
0.225
AC XY:
338
AN XY:
1502
show subpopulations
Gnomad4 AFR exome
AF:
0.400
Gnomad4 AMR exome
AF:
0.269
Gnomad4 ASJ exome
AF:
0.167
Gnomad4 EAS exome
AF:
0.530
Gnomad4 SAS exome
AF:
0.367
Gnomad4 FIN exome
AF:
0.107
Gnomad4 NFE exome
AF:
0.213
Gnomad4 OTH exome
AF:
0.222
GnomAD4 genome
AF:
0.253
AC:
38398
AN:
151798
Hom.:
5600
Cov.:
30
AF XY:
0.255
AC XY:
18901
AN XY:
74176
show subpopulations
Gnomad4 AFR
AF:
0.341
Gnomad4 AMR
AF:
0.261
Gnomad4 ASJ
AF:
0.127
Gnomad4 EAS
AF:
0.561
Gnomad4 SAS
AF:
0.342
Gnomad4 FIN
AF:
0.162
Gnomad4 NFE
AF:
0.187
Gnomad4 OTH
AF:
0.228
Alfa
AF:
0.218
Hom.:
744
Bravo
AF:
0.262
Asia WGS
AF:
0.436
AC:
1514
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
4.2
DANN
Benign
0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs73437201; hg19: chr7-69063900; API