chrX-141259689-T-G

Position:

• chrX-141259689-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662492.1(SPANXA2-OT1):​n.102+71852T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 111,518 control chromosomes in the GnomAD database, including 1,048 homozygotes. There are 5,230 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 0.16 (1048 hom., 5230 hem., cov: 24)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+71852T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.160 AC: 17858 AN: 111465 Hom.: 1050 Cov.: 24 AF XY: 0.155 AC XY: 5222 AN XY: 33671

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.160 AC: 17866 AN: 111518 Hom.: 1048 Cov.: 24 AF XY: 0.155 AC XY: 5230 AN XY: 33734

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0831 Hom.: 390

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881223; hg19: chrX-140353820;