chrX-141256320-T-C

Position:

• chrX-141256320-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000662492.1(SPANXA2-OT1):​n.102+68483T>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 0.75 (22105 hom., 23930 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=6.931).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+68483T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.754 AC: 82436 AN: 109338 Hom.: 22118 Cov.: 22 AF XY: 0.754 AC XY: 23885 AN XY: 31690

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.776

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: 0.754 AC: 82464 AN: 109386 Hom.: 22105 Cov.: 22 AF XY: 0.754 AC XY: 23930 AN XY: 31748

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.775

Alfa AF: 0.773 Hom.: 6403

Bravo AF: 0.749

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845144; hg19: -;