chrX-100660565-C-T

Position:

• chrX-100660565-C-T

Variant summary

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

The NM_014467.3(SRPX2):​c.164-1611C>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 0.64 (17126 hom., 20749 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRPX2	NM_014467.3	c.164-1611C>T		intron_variant		ENST00000373004.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-1611C>T		intron_variant		1	NM_014467.3	P1

Frequencies

GnomAD3 genomes AF: 0.638 AC: 70511 AN: 110485 Hom.: 17139 Cov.: 23 AF XY: 0.630 AC XY: 20724 AN XY: 32915

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.776

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: 0.638 AC: 70515 AN: 110537 Hom.: 17126 Cov.: 23 AF XY: 0.629 AC XY: 20749 AN XY: 32977

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.670

Alfa AF: 0.701 Hom.: 5663

Bravo AF: 0.628

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.84

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: rs36224192; hg19: chrX-99915562;