X-141258998-A-G

Position:

• chrX-141258998-A-G

Variant summary

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

The ENST00000662492.1(SPANXA2-OT1):​n.102+71161A>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 0.90 (31456 hom., 29323 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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=-0.86).

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+71161A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.897 AC: 98998 AN: 110353 Hom.: 31465 Cov.: 23 AF XY: 0.899 AC XY: 29271 AN XY: 32571

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.994

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.912

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: 0.897 AC: 99037 AN: 110403 Hom.: 31456 Cov.: 23 AF XY: 0.899 AC XY: 29323 AN XY: 32631

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.940

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.910

Alfa AF: 0.931 Hom.: 26760

Bravo AF: 0.897

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845150; hg19: chrX-140353129;