X-141284214-T-C

Position:

• chrX-141284214-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+96377T>C variant causes a intron 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 0.67 (17477 hom., 21268 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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 (BayesDel_noAF=-0.88).

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+96377T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.665 AC: 73137 AN: 109996 Hom.: 17469 Cov.: 22 AF XY: 0.657 AC XY: 21212 AN XY: 32286

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.652

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: 0.665 AC: 73202 AN: 110044 Hom.: 17477 Cov.: 22 AF XY: 0.658 AC XY: 21268 AN XY: 32344

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.654

Alfa AF: 0.671 Hom.: 6585

Bravo AF: 0.662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845186; hg19: chrX-140378356;