X-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTT

Variant names:

• chrX-100661933-G-GT
• rs771852530
• NM_014467.3:c.164-217dupT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_014467.3(SRPX2):​c.164-217dupT 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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.164-217dupT		intron_variant	Intron 3 of 10	ENST00000373004.5	NP_055282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-243_164-242insT		intron_variant	Intron 3 of 10	1	NM_014467.3	ENSP00000362095.3

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 2739 AN: 59636 Hom.: 319 Cov.: 16

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

African (AFR) AF: 0.0587 AC: 826 AN: 14079

American (AMR) AF: 0.0202 AC: 108 AN: 5357

Ashkenazi Jewish (ASJ) AF: 0.0509 AC: 85 AN: 1670

East Asian (EAS) AF: 0.0187 AC: 35 AN: 1869

South Asian (SAS) AF: 0.0130 AC: 15 AN: 1158

European-Finnish (FIN) AF: 0.00303 AC: 5 AN: 1649

Middle Eastern (MID) AF: 0.0297 AC: 3 AN: 101

European-Non Finnish (NFE) AF: 0.0492 AC: 1599 AN: 32499

Other (OTH) AF: 0.0612 AC: 50 AN: 817

Alfa AF: 0.00516 Hom.: 27

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 21, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.015
Mutation Taster		=100/0	polymorphism (auto)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs771852530; hg19: chrX-99916930;