7-69599743-GGGGGCCGGCGCGGCCGGCGGCGGC-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_015570(AUTS2):c.96_119del(p.Ala34_Gly41del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

AUTS2
NM_015570 inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.23

Links

AUTS2 (HGNC:14262):

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 32.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AUTS2	NM_015570.4 linkuse as main transcript	c.96_119del	p.Ala34_Gly41del	inframe_deletion	1/19	ENST00000342771.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AUTS2	ENST00000342771.10 linkuse as main transcript	c.96_119del	p.Ala34_Gly41del	inframe_deletion	1/19	1	NM_015570.4	P4	Q8WXX7-1
AUTS2	ENST00000403018.3 linkuse as main transcript	c.96_119del	p.Ala34_Gly41del	inframe_deletion	1/5	1			Q8WXX7-3
AUTS2	ENST00000406775.6 linkuse as main transcript	c.96_119del	p.Ala34_Gly41del	inframe_deletion	1/18	1			Q8WXX7-2
AUTS2	ENST00000644939.1 linkuse as main transcript	c.96_119del	p.Ala34_Gly41del	inframe_deletion	1/19			A1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000250

AC:

AN:

1198688

Hom.:

AF XY:

0.00000343

AC XY:

AN XY:

582498

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:

0.0000524

Gnomad4 NFE exome

AF:

0.00000101

Gnomad4 OTH exome

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2022

Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 8 amino acids in a non-repeat region; In silico analysis supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over