X-100661311-C-T

Position:

• chrX-100661311-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000373004.5(SRPX2):​c.164-865C>T 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 0.89 (30759 hom., 28942 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SRPX2 ENST00000373004.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.164-865C>T		intron_variant		ENST00000373004.5	NP_055282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-865C>T		intron_variant		1	NM_014467.3	ENSP00000362095	P1

Frequencies

GnomAD3 genomes AF: 0.886 AC: 98007 AN: 110660 Hom.: 30766 Cov.: 23 AF XY: 0.880 AC XY: 28890 AN XY: 32846

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.920

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.910

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: 0.886 AC: 98046 AN: 110711 Hom.: 30759 Cov.: 23 AF XY: 0.880 AC XY: 28942 AN XY: 32907

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.908

Alfa AF: 0.908 Hom.: 69403

Bravo AF: 0.892

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.44

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: rs5921619; hg19: chrX-99916308;