X-141259689-T-G

Variant names:

• chrX-141259689-T-G
• rs881223
• ENST00000662492.1:n.102+71852T>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+71852T>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.179 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+71852T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 17858 AN: 111465 Hom.: 1050 Cov.: 24

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

African (AFR) AF: 0.152 AC: 4673 AN: 30770

American (AMR) AF: 0.172 AC: 1800 AN: 10479

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 403 AN: 2645

East Asian (EAS) AF: 0.127 AC: 450 AN: 3541

South Asian (SAS) AF: 0.193 AC: 524 AN: 2715

European-Finnish (FIN) AF: 0.193 AC: 1151 AN: 5963

Middle Eastern (MID) AF: 0.145 AC: 31 AN: 214

European-Non Finnish (NFE) AF: 0.157 AC: 8336 AN: 52994

Other (OTH) AF: 0.145 AC: 221 AN: 1522

Alfa AF: 0.0831 Hom.: 390

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.62
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs881223; hg19: chrX-140353820;