chrX-141282112-T-G

Variant names:

• chrX-141282112-T-G
• rs845190
• ENST00000662492.1:n.102+94275T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662492.1(SPANXA2-OT1):​n.102+94275T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 109,426 control chromosomes in the GnomAD database, including 9,095 homozygotes. There are 14,608 hemizygotes in GnomAD. 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 0.47 (9095 hom., 14608 hem., cov: 22)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

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+94275T>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.471 AC: 51464 AN: 109374 Hom.: 9095 Cov.: 22

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.447

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.471 AC: 51491 AN: 109426 Hom.: 9095 Cov.: 22 AF XY: 0.459 AC XY: 14608 AN XY: 31792

African (AFR) AF: 0.426 AC: 12786 AN: 30030

American (AMR) AF: 0.321 AC: 3295 AN: 10263

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1434 AN: 2611

East Asian (EAS) AF: 0.284 AC: 971 AN: 3413

South Asian (SAS) AF: 0.290 AC: 752 AN: 2591

European-Finnish (FIN) AF: 0.525 AC: 2957 AN: 5628

Middle Eastern (MID) AF: 0.514 AC: 110 AN: 214

European-Non Finnish (NFE) AF: 0.534 AC: 28027 AN: 52532

Other (OTH) AF: 0.443 AC: 656 AN: 1481

Alfa AF: 0.484 Hom.: 21247

Bravo AF: 0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.033
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs845190; hg19: chrX-140376252;