rs36224191

Variant names:

• chrX-100660556-G-A
• rs36224191
• NM_014467.3:c.164-1620G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-100660556-G-A
• chrX-100660556-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_014467.3(SRPX2):​c.164-1620G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.64 (17129 hom., 20691 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• rolandic epilepsy-speech dyspraxia syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• polymicrogyria, bilateral perisylvian, X-linked

  Inheritance: XL Classification: LIMITED Submitted by: G2P
• rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked

  Inheritance: XL Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.164-1620G>A		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.164-1620G>A		intron_variant	Intron 3 of 10	1	NM_014467.3	ENSP00000362095.3

Frequencies

GnomAD3 genomes AF: 0.638 AC: 70452 AN: 110470 Hom.: 17142 Cov.: 23

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.674

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.637 AC: 70457 AN: 110522 Hom.: 17129 Cov.: 23 AF XY: 0.628 AC XY: 20691 AN XY: 32952

African (AFR) AF: 0.375 AC: 11420 AN: 30420

American (AMR) AF: 0.660 AC: 6877 AN: 10417

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2109 AN: 2624

East Asian (EAS) AF: 0.578 AC: 2025 AN: 3502

South Asian (SAS) AF: 0.517 AC: 1375 AN: 2660

European-Finnish (FIN) AF: 0.696 AC: 4031 AN: 5789

Middle Eastern (MID) AF: 0.808 AC: 173 AN: 214

European-Non Finnish (NFE) AF: 0.775 AC: 40874 AN: 52717

Other (OTH) AF: 0.670 AC: 1009 AN: 1505

Alfa AF: 0.631 Hom.: 17719

Bravo AF: 0.628

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.61
PhyloP100		-0.24
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

Other links and lift over

dbSNP: rs36224191; hg19: chrX-99915553;