7-69599664-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_015570(AUTS2):c.11C>T(p.Pro4Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00289 in 152036 control chromosomes in the gnomAD Genomes database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0029 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 1 hom. )

Consequence

AUTS2
NM_015570 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 5.82

Links

AUTS2 (HGNC:14262):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038175583).

BP6

Variant 7:69599664-C>T is Benign according to our data. Variant chr7-69599664-C-T is described in ClinVar as [Benign]. Clinvar id is 975656. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-69599664-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected. gnomad allele frequency = 0.00289 (440/152036) while in subpopulation NFE AF= 0.00512 (348/67974). AF 95% confidence interval is 0.00468. There are 2 homozygotes in gnomad. There are 177 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd at 440 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AUTS2	NM_015570.4 linkuse as main transcript	c.11C>T	p.Pro4Leu	missense_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.11C>T	p.Pro4Leu	missense_variant	1/19	1	NM_015570.4	P4	Q8WXX7-1
AUTS2	ENST00000406775.6 linkuse as main transcript	c.11C>T	p.Pro4Leu	missense_variant	1/18	1			Q8WXX7-2
AUTS2	ENST00000403018.3 linkuse as main transcript	c.11C>T	p.Pro4Leu	missense_variant	1/5	1			Q8WXX7-3
AUTS2	ENST00000644939.1 linkuse as main transcript	c.11C>T	p.Pro4Leu	missense_variant	1/19			A1

Frequencies

GnomAD3 genomes

AF:

0.00289

AC:

440

AN:

152036

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000845

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00124

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000660

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00512

Gnomad OTH

AF:

0.00384

GnomAD3 exomes

AF:

0.00341

AC:

AN:

11154

Hom.:

AF XY:

0.00368

AC XY:

AN XY:

5974

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00610

Gnomad ASJ exome

AF:

0.0101

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000211

Gnomad NFE exome

AF:

0.00609

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.00483

AC:

5563

AN:

1152222

Hom.:

AF XY:

0.00471

AC XY:

2610

AN XY:

554422

show subpopulations

Gnomad4 AFR exome

AF:

0.000990

Gnomad4 AMR exome

AF:

0.00197

Gnomad4 ASJ exome

AF:

0.00533

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000280

Gnomad4 FIN exome

AF:

0.000544

Gnomad4 NFE exome

AF:

0.00546

Gnomad4 OTH exome

AF:

0.00335

Alfa

AF:

0.00434

Hom.:

Bravo

AF:

0.00296

ExAC

AF:

0.000722

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg	Mar 21, 2023	This variant has been identified by standard clinical testing. -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	Criteria applied: PP2, BS1, BS2 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Oct 31, 2022	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 28, 2018	- -

Intellectual disability

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille

Jan 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.25

Cadd

Pathogenic

Dann

Uncertain

1.0

Eigen

Uncertain

0.47

Eigen_PC

Uncertain

0.43

FATHMM_MKL

Uncertain

0.82

LIST_S2

Benign

0.76

T;T;T;T

MetaRNN

Benign

0.0038

T;T;T;T

MetaSVM

Benign

-0.83

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Pathogenic

0.92

Polyphen

1.0

.;D;D;.

Vest4

0.38, 0.37, 0.47

MVP

0.47

MPC

2.6

ClinPred

0.067

GERP RS

3.6

Varity_R

0.25

gMVP

0.16

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