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GeneBe

7-69598633-A-AGCG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015570(AUTS2):c.-1003_-1001dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 128144 control chromosomes in the gnomAD Genomes database, including 71 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 71 hom., cov: 30)

Consequence

AUTS2
NM_015570 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.05

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 7:69598633-A>AGCG is Benign according to our data. Variant chr7-69598633-A-AGCG is described in ClinVar as [Benign]. Clinvar id is 1290296. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AUTS2NM_015570.4 linkuse as main transcriptc.-1003_-1001dup 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.-1003_-1001dup 5_prime_UTR_variant 1/191 NM_015570.4 P4Q8WXX7-1
AUTS2ENST00000644939.1 linkuse as main transcriptc.-1003_-1001dup 5_prime_UTR_variant 1/19 A1

Frequencies

GnomAD3 genomes
AF:
0.0202
AC:
2587
AN:
128144
Hom.:
71
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0714
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00985
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00132
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0120
Gnomad NFE
AF:
0.000135
Gnomad OTH
AF:
0.0126
GnomAD4 exome
AF:
0.00112
AC:
23
AN:
20604
Hom.:
0
AF XY:
0.000837
AC XY:
11
AN XY:
13144
show subpopulations
Gnomad4 AFR exome
AF:
0.0833
Gnomad4 AMR exome
AF:
0.0143
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000420
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000378
Gnomad4 OTH exome
AF:
0.00229

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 testingGeneDxApr 17, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs572172462; hg19: chr7-69063619;