X-100661933-G-GTT

Variant names:

• chrX-100661933-G-GTT
• rs771852530
• NM_014467.3:c.164-218_164-217dupTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_014467.3(SRPX2):​c.164-218_164-217dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.013 (60 hom., 76 hem., cov: 16)
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

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

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0134 (801/59692) while in subpopulation AFR AF = 0.0222 (313/14104). AF 95% confidence interval is 0.0202. There are 60 homozygotes in GnomAd4. There are 76 alleles in the male GnomAd4 subpopulation. Median coverage is 16. This position passed quality control check.
• BS2: High AC in GnomAd4 at 801 XLR,XL,AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.164-218_164-217dupTT		intron_variant	Intron 3 of 10	ENST00000373004.5	NP_055282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-243_164-242insTT		intron_variant	Intron 3 of 10	1	NM_014467.3	ENSP00000362095.3

Frequencies

GnomAD3 genomes AF: 0.0134 AC: 801 AN: 59681 Hom.: 60 Cov.: 16

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.00223

Gnomad AMR AF: 0.00504

Gnomad ASJ AF: 0.00239

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00182

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0149

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

GnomAD4 genome AF: 0.0134 AC: 801 AN: 59692 Hom.: 60 Cov.: 16 AF XY: 0.00575 AC XY: 76 AN XY: 13226

African (AFR) AF: 0.0222 AC: 313 AN: 14104

American (AMR) AF: 0.00503 AC: 27 AN: 5363

Ashkenazi Jewish (ASJ) AF: 0.00239 AC: 4 AN: 1672

East Asian (EAS) AF: 0.00 AC: 0 AN: 1868

South Asian (SAS) AF: 0.00 AC: 0 AN: 1159

European-Finnish (FIN) AF: 0.00182 AC: 3 AN: 1650

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 101

European-Non Finnish (NFE) AF: 0.0136 AC: 441 AN: 32508

Other (OTH) AF: 0.0147 AC: 12 AN: 818

Alfa AF: 0.000818 Hom.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.015
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs771852530; hg19: chrX-99916930;