rs5907859

Positions:

• chrX-141268958-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+81121C>T		intron_variant, non_coding_transcript_variant

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;