X-141356084-A-G

Position:

• chrX-141356084-A-G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.103-137067A>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 0.235 in 110,529 control chromosomes in the GnomAD database, including 2,673 homozygotes. There are 7,461 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 0.24 (2673 hom., 7461 hem., cov: 22)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

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 (Cadd=2.272).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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.103-137067A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.235 AC: 26005 AN: 110474 Hom.: 2675 Cov.: 22 AF XY: 0.227 AC XY: 7448 AN XY: 32766

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.235 AC: 26009 AN: 110529 Hom.: 2673 Cov.: 22 AF XY: 0.227 AC XY: 7461 AN XY: 32831

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0175

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.263

Alfa AF: 0.286 Hom.: 9805

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844956; hg19: -;