rs845189

chrX-141282725-A-GchrX-141282725-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000662492.1(SPANXA2-OT1):n.102+94888A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.52 (10770 hom., 15990 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=3.101).
• BS2: High Homozygotes in GnomAd at 10778 gene

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+94888A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.521 AC: 56647 AN: 108817 Hom.: 10778 Cov.: 21 AF XY: 0.512 AC XY: 15964 AN XY: 31183

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.527

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.520 AC: 56655 AN: 108874 Hom.: 10770 Cov.: 21 AF XY: 0.512 AC XY: 15990 AN XY: 31250

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.524

Alfa AF: 0.498 Hom.: 21562

Bravo AF: 0.526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	3.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845189; hg19: -;