X-141283020-G-C

Variant names:

• chrX-141283020-G-C
• rs845187
• ENST00000662492.1:n.102+95183G>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+95183G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 109,948 control chromosomes in the GnomAD database, including 1,561 homozygotes. There are 5,362 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 0.18 (1561 hom., 5362 hem., cov: 22)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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+95183G>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.179 AC: 19692 AN: 109889 Hom.: 1560 Cov.: 22

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.00514

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 19725 AN: 109948 Hom.: 1561 Cov.: 22 AF XY: 0.166 AC XY: 5362 AN XY: 32290

African (AFR) AF: 0.273 AC: 8218 AN: 30126

American (AMR) AF: 0.115 AC: 1179 AN: 10233

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 477 AN: 2636

East Asian (EAS) AF: 0.00516 AC: 18 AN: 3488

South Asian (SAS) AF: 0.0619 AC: 159 AN: 2567

European-Finnish (FIN) AF: 0.130 AC: 749 AN: 5742

Middle Eastern (MID) AF: 0.236 AC: 50 AN: 212

European-Non Finnish (NFE) AF: 0.159 AC: 8404 AN: 52787

Other (OTH) AF: 0.189 AC: 281 AN: 1488

Alfa AF: 0.170 Hom.: 974

Bravo AF: 0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs845187; hg19: chrX-140377162;