X-100661933-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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

• Frequency: Genomes: 𝑓 0.046 (319 hom., 237 hem., cov: 16)
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0150

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-100661933-G-GT is Benign according to our data. Variant chrX-100661933-G-GT is described in ClinVar as [Benign]. Clinvar id is 1236829.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRPX2	NM_014467.3	c.164-217dup		intron_variant		ENST00000373004.5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 2739 AN: 59636 Hom.: 319 Cov.: 16 AF XY: 0.0180 AC XY: 237 AN XY: 13184

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0290

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0509

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.00303

Gnomad MID AF: 0.0261

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.0620

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

GnomAD4 genome AF: 0.0459 AC: 2739 AN: 59647 Hom.: 319 Cov.: 16 AF XY: 0.0180 AC XY: 237 AN XY: 13191

Gnomad4 AFR AF: 0.0587

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.0509

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.00303

Gnomad4 NFE AF: 0.0492

Gnomad4 OTH AF: 0.0612

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs771852530; hg19: chrX-99916930;