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GeneBe

7-69598673-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2

The NM_015570(AUTS2):c.-981T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 152026 control chromosomes in the gnomAD Genomes database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 3 hom., cov: 30)

Consequence

AUTS2
NM_015570 5_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.378

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 7:69598673-T>C is Benign according to our data. Variant chr7-69598673-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1199522. Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.00372 (565/152026) while in subpopulation AFR AF= 0.00987 (409/41424). AF 95% confidence interval is 0.00908. There are 3 homozygotes in gnomad. There are 277 alleles in male gnomad subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 565 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AUTS2NM_015570.4 linkuse as main transcriptc.-981T>C 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.-981T>C 5_prime_UTR_variant 1/191 NM_015570.4 P4Q8WXX7-1
AUTS2ENST00000644939.1 linkuse as main transcriptc.-981T>C 5_prime_UTR_variant 1/19 A1

Frequencies

GnomAD3 genomes
AF:
0.00372
AC:
565
AN:
152026
Hom.:
3
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00987
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00667
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.000603
Gnomad OTH
AF:
0.00433
GnomAD4 exome
AF:
0.000134
AC:
1
AN:
7450
Hom.:
0
AF XY:
0.000187
AC XY:
1
AN XY:
5360
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000188
Gnomad4 OTH exome
AF:
0.00
Alfa
AF:
0.00233
Hom.:
1
Bravo
AF:
0.00419
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJun 24, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
19
Dann
Benign
0.76

Splicing

Find out SpliceAI 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: rs535154040; hg19: chr7-69063659;