rs1493189

Variant names:

• chrX-141291826-A-G
• rs1493189
• ENST00000662492.1:n.102+103989A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662492.1(SPANXA2-OT1):​n.102+103989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 111,080 control chromosomes in the GnomAD database, including 904 homozygotes. There are 4,258 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 0.14 (904 hom., 4258 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 1 publications found

Genes affected

SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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-OT1	ENST00000662492.1	n.102+103989A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 15084 AN: 111030 Hom.: 902 Cov.: 23

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.136 AC: 15112 AN: 111080 Hom.: 904 Cov.: 23 AF XY: 0.128 AC XY: 4258 AN XY: 33354

African (AFR) AF: 0.226 AC: 6901 AN: 30476

American (AMR) AF: 0.109 AC: 1137 AN: 10441

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 362 AN: 2633

East Asian (EAS) AF: 0.0239 AC: 84 AN: 3521

South Asian (SAS) AF: 0.0505 AC: 133 AN: 2635

European-Finnish (FIN) AF: 0.100 AC: 595 AN: 5922

Middle Eastern (MID) AF: 0.156 AC: 33 AN: 212

European-Non Finnish (NFE) AF: 0.104 AC: 5534 AN: 53040

Other (OTH) AF: 0.145 AC: 222 AN: 1527

Alfa AF: 0.121 Hom.: 773

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.56
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1493189; hg19: chrX-140385970;