X-141243602-G-T

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):n.102+55765G>T 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 0.0067 (3 hom., 0 hem., cov: 2)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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=-0.97).

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+55765G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 233 AN: 34216 Hom.: 3 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 7926 FAILED QC

Gnomad AFR AF: 0.00635

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00727

Gnomad ASJ AF: 0.00120

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.00870

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00663

Gnomad OTH AF: 0.00759

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: AS_VQSR AF: 0.00675 AC: 231 AN: 34232 Hom.: 3 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 7934

Gnomad4 AFR AF: 0.00634

Gnomad4 AMR AF: 0.00726

Gnomad4 ASJ AF: 0.00120

Gnomad4 EAS AF: 0.0227

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.00870

Gnomad4 NFE AF: 0.00649

Gnomad4 OTH AF: 0.00756

Alfa AF: 0.446 Hom.: 2950

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.43
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5953578; hg19: chrX-140337730;