chrX-100661173-T-A

Position:

• chrX-100661173-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014467.3(SRPX2):​c.164-1003T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 112,359 control chromosomes in the GnomAD database, including 113 homozygotes. There are 1,142 hemizygotes in GnomAD. 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 0.038 (113 hom., 1142 hem., cov: 24)
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRPX2	NM_014467.3	c.164-1003T>A		intron_variant		ENST00000373004.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-1003T>A		intron_variant		1	NM_014467.3	P1

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 4289 AN: 112305 Hom.: 113 Cov.: 24 AF XY: 0.0331 AC XY: 1140 AN XY: 34469

Gnomad AFR AF: 0.00831

Gnomad AMI AF: 0.00871

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.00195

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0264

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

GnomAD4 genome AF: 0.0382 AC: 4289 AN: 112359 Hom.: 113 Cov.: 24 AF XY: 0.0331 AC XY: 1142 AN XY: 34533

Gnomad4 AFR AF: 0.00830

Gnomad4 AMR AF: 0.0210

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.00195

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0261

Alfa AF: 0.0546 Hom.: 284

Bravo AF: 0.0354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.077
DANN	Benign	0.69

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: rs36224184; hg19: chrX-99916170;