Variant chrX-100661933-GT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_014467.3(SRPX2):c.164-217del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.035 ( 55 hom., 138 hem., cov: 16)

Consequence

SRPX2
NM_014467.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0150

Variant links:

Genes affected

SRPX2 (HGNC:30668): (sushi repeat containing protein X-linked 2) This gene encodes a secreted protein that contains three sushi repeat motifs. The encoded protein may play a role in the development of speech and language centers in the brain. This protein may also be involved in angiogenesis. Mutations in this gene are the cause of bilateral perisylvian polymicrogyria, rolandic epilepsy, speech dyspraxia and cognitive disability. [provided by RefSeq, May 2010]

SRPX2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-100661933-GT-G is Benign according to our data. Variant chrX-100661933-GT-G is described in ClinVar as [Benign]. Clinvar id is 1271515.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRPX2	NM_014467.3 linkuse as main transcript	c.164-217del		intron_variant		ENST00000373004.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRPX2	ENST00000373004.5 linkuse as main transcript	c.164-217del		intron_variant		1	NM_014467.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0349

AC:

2080

AN:

59634

Hom.:

Cov.:

AF XY:

0.0106

AC XY:

140

AN XY:

13170

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.00223

Gnomad AMR

AF:

0.0106

Gnomad ASJ

AF:

0.0240

Gnomad EAS

AF:

0.00267

Gnomad SAS

AF:

0.00172

Gnomad FIN

AF:

0.00364

Gnomad MID

AF:

0.0174

Gnomad NFE

AF:

0.0160

Gnomad OTH

AF:

0.0186

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0348

AC:

2077

AN:

59646

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

138

AN XY:

13178

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.0106

Gnomad4 ASJ

AF:

0.0240

Gnomad4 EAS

AF:

0.00267

Gnomad4 SAS

AF:

0.00173

Gnomad4 FIN

AF:

0.00364

Gnomad4 NFE

AF:

0.0160

Gnomad4 OTH

AF:

0.0183

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

Dec 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over