rs714076

Variant names:

• chrX-141256871-T-C
• rs714076
• ENST00000662492.1:n.102+69034T>C

Your query was ambiguous. Multiple possible variants found:

• chrX-141256871-T-C
• chrX-141256871-T-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.102+69034T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 110,551 control chromosomes in the GnomAD database, including 2,292 homozygotes. There are 7,784 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 0.24 (2292 hom., 7784 hem., cov: 22)
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 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+69034T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.242 AC: 26708 AN: 110501 Hom.: 2293 Cov.: 22

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.242 AC: 26722 AN: 110551 Hom.: 2292 Cov.: 22 AF XY: 0.237 AC XY: 7784 AN XY: 32813

African (AFR) AF: 0.241 AC: 7348 AN: 30434

American (AMR) AF: 0.258 AC: 2677 AN: 10365

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 714 AN: 2638

East Asian (EAS) AF: 0.143 AC: 499 AN: 3500

South Asian (SAS) AF: 0.217 AC: 569 AN: 2620

European-Finnish (FIN) AF: 0.287 AC: 1653 AN: 5757

Middle Eastern (MID) AF: 0.215 AC: 46 AN: 214

European-Non Finnish (NFE) AF: 0.238 AC: 12590 AN: 52843

Other (OTH) AF: 0.221 AC: 334 AN: 1510

Alfa AF: 0.244 Hom.: 1550

Bravo AF: 0.245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs714076; hg19: chrX-140351000;