X-141352691-A-G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.103-140460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 110,660 control chromosomes in the GnomAD database, including 3,667 homozygotes. There are 9,047 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 0.29 ( 3667 hom., 9047 hem., cov: 23)

Consequence

SPANXA2-OT1
ENST00000662492.1 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.384
Variant links:
Genes affected
SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPANXA2-OT1ENST00000662492.1 linkn.103-140460A>G intron_variant Intron 2 of 5

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
31816
AN:
110604
Hom.:
3667
Cov.:
23
AF XY:
0.275
AC XY:
9025
AN XY:
32878
show subpopulations
Gnomad AFR
AF:
0.398
Gnomad AMI
AF:
0.135
Gnomad AMR
AF:
0.195
Gnomad ASJ
AF:
0.338
Gnomad EAS
AF:
0.0187
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.295
Gnomad MID
AF:
0.309
Gnomad NFE
AF:
0.267
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.288
AC:
31835
AN:
110660
Hom.:
3667
Cov.:
23
AF XY:
0.275
AC XY:
9047
AN XY:
32944
show subpopulations
Gnomad4 AFR
AF:
0.398
Gnomad4 AMR
AF:
0.194
Gnomad4 ASJ
AF:
0.338
Gnomad4 EAS
AF:
0.0190
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.295
Gnomad4 NFE
AF:
0.267
Gnomad4 OTH
AF:
0.301
Alfa
AF:
0.298
Hom.:
1977
Bravo
AF:
0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.81

Splicing

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: rs844963; hg19: chrX-140446840; API