X-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTT

Variant names:

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

Variant summary

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

The NM_014467.3(SRPX2):​c.164-217delT 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
• 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-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 rank	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.164-217delT		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.164-242delT		intron_variant	Intron 3 of 10	1	NM_014467.3	ENSP00000362095.3

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 2080 AN: 59634 Hom.: 55 Cov.: 16

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.: 55 Cov.: 16 AF XY: 0.0105 AC XY: 138 AN XY: 13178

African (AFR) AF: 0.102 AC: 1428 AN: 14068

American (AMR) AF: 0.0106 AC: 57 AN: 5364

Ashkenazi Jewish (ASJ) AF: 0.0240 AC: 40 AN: 1669

East Asian (EAS) AF: 0.00267 AC: 5 AN: 1870

South Asian (SAS) AF: 0.00173 AC: 2 AN: 1159

European-Finnish (FIN) AF: 0.00364 AC: 6 AN: 1650

Middle Eastern (MID) AF: 0.0198 AC: 2 AN: 101

European-Non Finnish (NFE) AF: 0.0160 AC: 521 AN: 32498

Other (OTH) AF: 0.0183 AC: 15 AN: 818

Alfa AF: 0.00239 Hom.: 27

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 10, 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

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;