7-69599223-A-G

Variant summary

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

The NM_015570(AUTS2):c.-431A>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 0.00163 in 140816 control chromosomes in the gnomAD Genomes database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 1 hom., cov: 31)

Consequence

AUTS2
NM_015570 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.991

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=-0.35).

BP6

Variant 7:69599223-A>G is Benign according to our data. Variant chr7-69599223-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1195316. Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected. gnomad allele frequency = 0.00163 (230/140816) while in subpopulation NFE AF= 0.00042 (27/64212). AF 95% confidence interval is 0.000296. There are 1 homozygotes in gnomad. There are 175 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd at 230 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AUTS2	NM_015570.4 linkuse as main transcript	c.-431A>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.-431A>G	5_prime_UTR_variant	1/19	1	NM_015570.4	P4	Q8WXX7-1
AUTS2	ENST00000406775.6 linkuse as main transcript	c.-431A>G	5_prime_UTR_variant	1/18	1			Q8WXX7-2
AUTS2	ENST00000644939.1 linkuse as main transcript	c.-431A>G	5_prime_UTR_variant	1/19			A1

Frequencies

GnomAD3 genomes

AF:

0.00163

AC:

230

AN:

140816

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0232

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000420

Gnomad OTH

AF:

0.00

Alfa

AF:

0.00116

Hom.:

Bravo

AF:

0.0000453

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

Sep 29, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

Cadd

Benign

Dann

Benign

0.89

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