chrX-141289406-A-C

Variant names:

• chrX-141289406-A-C
• rs5907874
• ENST00000662492.1:n.102+101569A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662492.1(SPANXA2-OT1):​n.102+101569A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 110,669 control chromosomes in the GnomAD database, including 3,829 homozygotes. There are 9,980 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 0.31 (3829 hom., 9980 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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+101569A>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.308 AC: 34083 AN: 110614 Hom.: 3831 Cov.: 23 AF XY: 0.303 AC XY: 9983 AN XY: 32910

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.308 AC: 34068 AN: 110669 Hom.: 3829 Cov.: 23 AF XY: 0.303 AC XY: 9980 AN XY: 32975

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.310

Alfa AF: 0.306 Hom.: 1948

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5907874; hg19: chrX-140383548;