rs55843102

Variant names:

• chrX-141265726-C-T
• rs55843102
• ENST00000662492.1:n.102+77889C>T

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+77889C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 110,652 control chromosomes in the GnomAD database, including 1,229 homozygotes. There are 5,407 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 0.17 (1229 hom., 5407 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPANXA2-OT1	ENST00000662492.1		n.102+77889C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 19131 AN: 110598 Hom.: 1231 Cov.: 23

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.173 AC: 19142 AN: 110652 Hom.: 1229 Cov.: 23 AF XY: 0.164 AC XY: 5407 AN XY: 32952

African (AFR) AF: 0.169 AC: 5132 AN: 30422

American (AMR) AF: 0.185 AC: 1913 AN: 10355

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 508 AN: 2623

East Asian (EAS) AF: 0.125 AC: 434 AN: 3485

South Asian (SAS) AF: 0.187 AC: 492 AN: 2638

European-Finnish (FIN) AF: 0.191 AC: 1115 AN: 5851

Middle Eastern (MID) AF: 0.167 AC: 36 AN: 215

European-Non Finnish (NFE) AF: 0.170 AC: 8996 AN: 52894

Other (OTH) AF: 0.159 AC: 240 AN: 1507

Alfa AF: 0.165 Hom.: 949

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.83
DANN	Benign	0.95
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs55843102;

hg19: chrX-140359868;