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7-69599651-A-G

Variant summary

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

The ENST00000406775.6(AUTS2):c.-3A>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 0.0846 in 1,297,190 control chromosomes in the GnomAD database, including 5,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1768 hom., cov: 32)
Exomes 𝑓: 0.079 ( 4036 hom. )

Consequence

AUTS2
ENST00000406775.6 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.04
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 7-69599651-A-G is Benign according to our data. Variant chr7-69599651-A-G is described in ClinVar as [Benign]. Clinvar id is 1178068.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AUTS2NM_015570.4 linkuse as main transcriptc.-3A>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.-3A>G 5_prime_UTR_variant 1/191 NM_015570.4 P4Q8WXX7-1
AUTS2ENST00000403018.3 linkuse as main transcriptc.-3A>G 5_prime_UTR_variant 1/51 Q8WXX7-3
AUTS2ENST00000406775.6 linkuse as main transcriptc.-3A>G 5_prime_UTR_variant 1/181 Q8WXX7-2
AUTS2ENST00000644939.1 linkuse as main transcriptc.-3A>G 5_prime_UTR_variant 1/19 A1

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19102
AN:
151634
Hom.:
1760
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.0177
Gnomad AMR
AF:
0.0760
Gnomad ASJ
AF:
0.0820
Gnomad EAS
AF:
0.0781
Gnomad SAS
AF:
0.0850
Gnomad FIN
AF:
0.0616
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0757
Gnomad OTH
AF:
0.106
GnomAD3 exomes
AF:
0.0568
AC:
497
AN:
8750
Hom.:
13
AF XY:
0.0576
AC XY:
263
AN XY:
4564
show subpopulations
Gnomad AFR exome
AF:
0.241
Gnomad AMR exome
AF:
0.0420
Gnomad ASJ exome
AF:
0.0694
Gnomad EAS exome
AF:
0.0286
Gnomad SAS exome
AF:
0.0645
Gnomad FIN exome
AF:
0.0459
Gnomad NFE exome
AF:
0.0666
Gnomad OTH exome
AF:
0.0672
GnomAD4 exome
AF:
0.0791
AC:
90660
AN:
1145448
Hom.:
4036
Cov.:
32
AF XY:
0.0790
AC XY:
43457
AN XY:
550410
show subpopulations
Gnomad4 AFR exome
AF:
0.263
Gnomad4 AMR exome
AF:
0.0766
Gnomad4 ASJ exome
AF:
0.0827
Gnomad4 EAS exome
AF:
0.0552
Gnomad4 SAS exome
AF:
0.0799
Gnomad4 FIN exome
AF:
0.0575
Gnomad4 NFE exome
AF:
0.0755
Gnomad4 OTH exome
AF:
0.0904
GnomAD4 genome
AF:
0.126
AC:
19136
AN:
151742
Hom.:
1768
Cov.:
32
AF XY:
0.124
AC XY:
9223
AN XY:
74176
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.0760
Gnomad4 ASJ
AF:
0.0820
Gnomad4 EAS
AF:
0.0779
Gnomad4 SAS
AF:
0.0843
Gnomad4 FIN
AF:
0.0616
Gnomad4 NFE
AF:
0.0757
Gnomad4 OTH
AF:
0.107
Alfa
AF:
0.0843
Hom.:
572
Bravo
AF:
0.134
Asia WGS
AF:
0.101
AC:
351
AN:
3476

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 03, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
CADD
Benign
19
DANN
Benign
0.83

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

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

Other links and lift over

dbSNP: rs3735260; hg19: chr7-69064637; API