rs5966711

chrX-100658727-C-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_014467.3(SRPX2):c.164-3449C>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 0.75 (22717 hom., 24986 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 22731 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRPX2	NM_014467.3	c.164-3449C>A		intron_variant		ENST00000373004.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-3449C>A		intron_variant		1	NM_014467.3	P1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 83186 AN: 110992 Hom.: 22731 Cov.: 23 AF XY: 0.751 AC XY: 24952 AN XY: 33210

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.871

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.764

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: 0.749 AC: 83202 AN: 111045 Hom.: 22717 Cov.: 23 AF XY: 0.751 AC XY: 24986 AN XY: 33273

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.762

Alfa AF: 0.801 Hom.: 6839

Bravo AF: 0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.66

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: rs5966711; hg19: chrX-99913724;