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

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.378

Links

AUTS2 (HGNC:14262):

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
AUTS2	NM_015570.4 linkuse as main transcript	c.-981T>C		5_prime_UTR_variant	1/19	ENST00000342771.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AUTS2	ENST00000342771.10 linkuse as main transcript	c.-981T>C		5_prime_UTR_variant	1/19	1	NM_015570.4	P4	Q8WXX7-1
AUTS2	ENST00000644939.1 linkuse as main transcript	c.-981T>C		5_prime_UTR_variant	1/19			A1

Frequencies

GnomAD3 genomes

AF:

0.00372

AC:

565

AN:

152026

Hom.:

Cov.:

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:

AN:

7450

Hom.:

AF XY:

0.000187

AC XY:

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.:

Bravo

AF:

0.00419

Asia WGS

AF:

0.000866

AC:

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 submitter

clinical testing

GeneDx

Jun 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

Cadd

Benign

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over