rs845189

Variant names:

• chrX-141282725-A-G
• rs845189
• ENST00000662492.1:n.102+94888A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-141282725-A-G
• chrX-141282725-A-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+94888A>G 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 0.52 (10770 hom., 15990 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 1 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 (Cadd=3.101).

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+94888A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.521 AC: 56647 AN: 108817 Hom.: 10778 Cov.: 21

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.527

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: 0.520 AC: 56655 AN: 108874 Hom.: 10770 Cov.: 21 AF XY: 0.512 AC XY: 15990 AN XY: 31250

African (AFR) AF: 0.598 AC: 17900 AN: 29946

American (AMR) AF: 0.478 AC: 4819 AN: 10078

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1423 AN: 2622

East Asian (EAS) AF: 0.450 AC: 1525 AN: 3391

South Asian (SAS) AF: 0.507 AC: 1266 AN: 2499

European-Finnish (FIN) AF: 0.530 AC: 2910 AN: 5490

Middle Eastern (MID) AF: 0.524 AC: 110 AN: 210

European-Non Finnish (NFE) AF: 0.487 AC: 25579 AN: 52488

Other (OTH) AF: 0.524 AC: 774 AN: 1477

Alfa AF: 0.511 Hom.: 37709

Bravo AF: 0.526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.1
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs845189; hg19: -;