chrX-141268958-C-T

Variant names:

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

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+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
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662492.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+81121C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 32138 AN: 110673 Hom.: 3481 Cov.: 23

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

African (AFR) AF: 0.312 AC: 9536 AN: 30540

American (AMR) AF: 0.270 AC: 2807 AN: 10382

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 856 AN: 2627

East Asian (EAS) AF: 0.126 AC: 441 AN: 3491

South Asian (SAS) AF: 0.223 AC: 599 AN: 2681

European-Finnish (FIN) AF: 0.321 AC: 1885 AN: 5880

Middle Eastern (MID) AF: 0.251 AC: 54 AN: 215

European-Non Finnish (NFE) AF: 0.289 AC: 15249 AN: 52724

Other (OTH) AF: 0.288 AC: 434 AN: 1509

Alfa AF: 0.289 Hom.: 2169

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.53
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs5907859; hg19: chrX-140363100;