chrX-100654343-G-T

Position:

• chrX-100654343-G-T

Variant summary

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

The ENST00000373004.5(SRPX2):​c.163+3478G>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 0.60 (15919 hom., 18968 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: SRPX2 ENST00000373004.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.163+3478G>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.163+3478G>T		intron_variant		1	NM_014467.3	ENSP00000362095.3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 66030 AN: 109492 Hom.: 15932 Cov.: 21 AF XY: 0.596 AC XY: 18950 AN XY: 31806

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.795

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.641

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: 0.603 AC: 66026 AN: 109544 Hom.: 15919 Cov.: 21 AF XY: 0.595 AC XY: 18968 AN XY: 31868

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.639

Alfa AF: 0.458 Hom.: 2373

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.76

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: rs6616171; hg19: chrX-99909340;