chrX-141268958-C-T

Variant names:

• chrX-141268958-C-T
• rs5907859
• ENST00000662492.1:n.102+81121C>T

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.102+81121C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 110,726 control chromosomes in the GnomAD database, including 3,480 homozygotes. There are 9,184 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 (3480 hom., 9184 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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+81121C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.290 AC: 32138 AN: 110673 Hom.: 3481 Cov.: 23 AF XY: 0.278 AC XY: 9160 AN XY: 33007

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.249

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.290 AC: 32164 AN: 110726 Hom.: 3480 Cov.: 23 AF XY: 0.278 AC XY: 9184 AN XY: 33070

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.288

Alfa AF: 0.289 Hom.: 2169

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5907859; hg19: chrX-140363100;