X-57069482-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000404529.2(SPIN2P1):n.204G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 218,768 control chromosomes in the GnomAD database, including 31,717 homozygotes. There are 41,077 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 0.55 (14504 hom., 18558 hem., cov: 23)
  • Exomes 𝑓: 0.66 (17213 hom. 22519 hem.)
• Consequence: SPIN2P1 ENST00000404529.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

SPIN2P1 (HGNC:54967): (SPIN2 family pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPIN2P1	ENST00000404529.2	n.204G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 61079 AN: 110861 Hom.: 14512 Cov.: 23 AF XY: 0.561 AC XY: 18557 AN XY: 33107

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.661 AC: 71336 AN: 107858 Hom.: 17213 Cov.: 0 AF XY: 0.647 AC XY: 22519 AN XY: 34832

Gnomad4 AFR exome AF: 0.112

Gnomad4 AMR exome AF: 0.490

Gnomad4 ASJ exome AF: 0.465

Gnomad4 EAS exome AF: 0.622

Gnomad4 SAS exome AF: 0.542

Gnomad4 FIN exome AF: 0.832

Gnomad4 NFE exome AF: 0.709

Gnomad4 OTH exome AF: 0.634

GnomAD4 genome AF: 0.550 AC: 61056 AN: 110910 Hom.: 14504 Cov.: 23 AF XY: 0.560 AC XY: 18558 AN XY: 33166

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.497

Alfa AF: 0.637 Hom.: 6294

Bravo AF: 0.508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	13
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs204165; hg19: chrX-57095915;