X-141243602-G-T

Variant names:

• chrX-141243602-G-T
• rs5953578
• ENST00000662492.1:n.102+55765G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1	n.102+55765G>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.00681 AC: 233 AN: 34216 Hom.: 3 Cov.: 2

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00634 AC: 80 AN: 12624

American (AMR) AF: 0.00726 AC: 22 AN: 3031

Ashkenazi Jewish (ASJ) AF: 0.00120 AC: 1 AN: 830

East Asian (EAS) AF: 0.0227 AC: 13 AN: 573

South Asian (SAS) AF: 0.0108 AC: 6 AN: 556

European-Finnish (FIN) AF: 0.00870 AC: 13 AN: 1495

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 35

European-Non Finnish (NFE) AF: 0.00649 AC: 93 AN: 14329

Other (OTH) AF: 0.00756 AC: 3 AN: 397

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs5953578; hg19: chrX-140337730;