rs5907874

Variant names:

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

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+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
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662492.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+101569A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 34083 AN: 110614 Hom.: 3831 Cov.: 23

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

African (AFR) AF: 0.292 AC: 8917 AN: 30523

American (AMR) AF: 0.335 AC: 3490 AN: 10411

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 798 AN: 2620

East Asian (EAS) AF: 0.415 AC: 1437 AN: 3463

South Asian (SAS) AF: 0.386 AC: 1018 AN: 2639

European-Finnish (FIN) AF: 0.352 AC: 2076 AN: 5899

Middle Eastern (MID) AF: 0.248 AC: 53 AN: 214

European-Non Finnish (NFE) AF: 0.297 AC: 15671 AN: 52710

Other (OTH) AF: 0.310 AC: 471 AN: 1519

Alfa AF: 0.306 Hom.: 1948

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.42
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs5907874; hg19: chrX-140383548;