X-141284214-T-C

Variant names:

• chrX-141284214-T-C
• rs845186
• ENST00000662492.1:n.102+96377T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000662492.1(SPANXA2-OT1):​n.102+96377T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.67 (17477 hom., 21268 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: SPANXA2-OT1 ENST00000662492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 1 publications found

Genes affected

SPANXA2-OT1 (HGNC:31683): (SPANXA2 overlapping transcript 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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+96377T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.665 AC: 73137 AN: 109996 Hom.: 17469 Cov.: 22

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.652

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.665 AC: 73202 AN: 110044 Hom.: 17477 Cov.: 22 AF XY: 0.658 AC XY: 21268 AN XY: 32344

African (AFR) AF: 0.675 AC: 20423 AN: 30272

American (AMR) AF: 0.620 AC: 6406 AN: 10335

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 1708 AN: 2625

East Asian (EAS) AF: 0.558 AC: 1898 AN: 3404

South Asian (SAS) AF: 0.574 AC: 1463 AN: 2547

European-Finnish (FIN) AF: 0.612 AC: 3550 AN: 5802

Middle Eastern (MID) AF: 0.684 AC: 145 AN: 212

European-Non Finnish (NFE) AF: 0.686 AC: 36117 AN: 52671

Other (OTH) AF: 0.654 AC: 987 AN: 1509

Alfa AF: 0.671 Hom.: 6585

Bravo AF: 0.662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs845186; hg19: chrX-140378356;