chrX-100655621-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014467.3(SRPX2):​c.163+4756C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 110,627 control chromosomes in the GnomAD database, including 113 homozygotes. There are 1,091 hemizygotes in GnomAD. 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 0.038 ( 113 hom., 1091 hem., cov: 22)

Consequence

SRPX2
NM_014467.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRPX2NM_014467.3 linkuse as main transcriptc.163+4756C>T intron_variant ENST00000373004.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRPX2ENST00000373004.5 linkuse as main transcriptc.163+4756C>T intron_variant 1 NM_014467.3 P1

Frequencies

GnomAD3 genomes
AF:
0.0382
AC:
4221
AN:
110582
Hom.:
113
Cov.:
22
AF XY:
0.0332
AC XY:
1089
AN XY:
32822
show subpopulations
Gnomad AFR
AF:
0.00843
Gnomad AMI
AF:
0.0541
Gnomad AMR
AF:
0.0175
Gnomad ASJ
AF:
0.0387
Gnomad EAS
AF:
0.000852
Gnomad SAS
AF:
0.0239
Gnomad FIN
AF:
0.0322
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0635
Gnomad OTH
AF:
0.0222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0382
AC:
4222
AN:
110627
Hom.:
113
Cov.:
22
AF XY:
0.0332
AC XY:
1091
AN XY:
32877
show subpopulations
Gnomad4 AFR
AF:
0.00841
Gnomad4 AMR
AF:
0.0175
Gnomad4 ASJ
AF:
0.0387
Gnomad4 EAS
AF:
0.000855
Gnomad4 SAS
AF:
0.0244
Gnomad4 FIN
AF:
0.0322
Gnomad4 NFE
AF:
0.0636
Gnomad4 OTH
AF:
0.0219
Alfa
AF:
0.0545
Hom.:
289
Bravo
AF:
0.0350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.9
DANN
Benign
0.48

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs41292472; hg19: chrX-99910618; API