rs844970

chrX-141344617-T-C

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):n.103-148534T>C 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 0.62 (15104 hom., 20814 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

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 (BayesDel_noAF=-0.86).
• BS2: High Homozygotes in GnomAd at 15116 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.103-148534T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.623 AC: 69083 AN: 110881 Hom.: 15116 Cov.: 23 AF XY: 0.627 AC XY: 20775 AN XY: 33123

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.627

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: 0.623 AC: 69105 AN: 110931 Hom.: 15104 Cov.: 23 AF XY: 0.627 AC XY: 20814 AN XY: 33185

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.623

Alfa AF: 0.637 Hom.: 15978

Bravo AF: 0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844970; hg19: chrX-140438761;