chrX-141207898-T-C

Variant names:

• chrX-141207898-T-C
• rs1012777
• ENST00000662492.1:n.102+20061T>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+20061T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 111,068 control chromosomes in the GnomAD database, including 1,432 homozygotes. There are 5,988 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 0.19 (1432 hom., 5988 hem., cov: 23)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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+20061T>C		intron_variant	Intron 2 of 5
SPANXA2-OT1	ENST00000664367.1	n.112-302T>C		intron_variant	Intron 2 of 2
SPANXA2-OT1	ENST00000665569.1	n.71-302T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 20967 AN: 111012 Hom.: 1432 Cov.: 23 AF XY: 0.180 AC XY: 5981 AN XY: 33224

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.189 AC: 20977 AN: 111068 Hom.: 1432 Cov.: 23 AF XY: 0.180 AC XY: 5988 AN XY: 33290

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.167

Alfa AF: 0.173 Hom.: 997

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012777; hg19: chrX-140302078;