chrX-141352691-A-G

Variant names:

• chrX-141352691-A-G
• rs844963
• ENST00000662492.1:n.103-140460A>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.103-140460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 110,660 control chromosomes in the GnomAD database, including 3,667 homozygotes. There are 9,047 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 0.29 (3667 hom., 9047 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.392 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.103-140460A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.288 AC: 31816 AN: 110604 Hom.: 3667 Cov.: 23

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.288 AC: 31835 AN: 110660 Hom.: 3667 Cov.: 23 AF XY: 0.275 AC XY: 9047 AN XY: 32944

African (AFR) AF: 0.398 AC: 12085 AN: 30385

American (AMR) AF: 0.194 AC: 2016 AN: 10370

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 885 AN: 2617

East Asian (EAS) AF: 0.0190 AC: 67 AN: 3523

South Asian (SAS) AF: 0.121 AC: 324 AN: 2672

European-Finnish (FIN) AF: 0.295 AC: 1719 AN: 5831

Middle Eastern (MID) AF: 0.300 AC: 63 AN: 210

European-Non Finnish (NFE) AF: 0.267 AC: 14133 AN: 52874

Other (OTH) AF: 0.301 AC: 451 AN: 1497

Alfa AF: 0.298 Hom.: 1977

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs844963; hg19: chrX-140446840;