7-69598914-T-G

Variant summary

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

The NM_015570(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 151680 control chromosomes in the gnomAD Genomes database, including 5597 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 5597 hom., cov: 30)

Consequence

AUTS2
NM_015570 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.158

Links

AUTS2 (HGNC:14262):

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

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AUTS2	NM_015570.4 linkuse as main transcript	c.-740T>G		5_prime_UTR_variant	1/19	ENST00000342771.10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AUTS2	ENST00000342771.10 linkuse as main transcript	c.-740T>G	5_prime_UTR_variant	1/19	1	NM_015570.4	P4	Q8WXX7-1
AUTS2	ENST00000644939.1 linkuse as main transcript	c.-740T>G	5_prime_UTR_variant	1/19			A1
AUTS2	ENST00000406775.6 linkuse as main transcript		upstream_gene_variant		1			Q8WXX7-2

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38371

AN:

151680

Hom.:

5597

Cov.:

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.:

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

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 submitter

clinical testing

GeneDx

Jul 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

Cadd

Benign

6.0

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.

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