X-141282112-T-G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):n.102+94275T>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 0.471 in 109,426 control chromosomes in the GnomAD database, including 9,095 homozygotes. There are 14,608 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 0.47 (9095 hom., 14608 hem., cov: 22)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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.102+94275T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.471 AC: 51464 AN: 109374 Hom.: 9095 Cov.: 22 AF XY: 0.459 AC XY: 14573 AN XY: 31730

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.471 AC: 51491 AN: 109426 Hom.: 9095 Cov.: 22 AF XY: 0.459 AC XY: 14608 AN XY: 31792

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.443

Alfa AF: 0.492 Hom.: 13925

Bravo AF: 0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.033

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845190; hg19: chrX-140376252;