X-56983705-C-T

Position:

• chrX-56983705-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000478405.1(SPIN3):​c.*204+561G>A variant causes a intron, NMD transcript 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 0.72 (20364 hom., 24216 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: SPIN3 ENST00000478405.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

SPIN3 (HGNC:27272): (spindlin family member 3) Enables methylated histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be integral component of membrane. Predicted to be active in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPIN3	NR_027139.2	n.766+561G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPIN3	ENST00000478405.1	c.*204+561G>A		intron_variant, NMD_transcript_variant		1
SPIN3	ENST00000640131.1	c.*204+561G>A		intron_variant, NMD_transcript_variant		1
SPIN3	ENST00000475785.7	c.*204+561G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.721 AC: 80174 AN: 111227 Hom.: 20368 Cov.: 24 AF XY: 0.723 AC XY: 24169 AN XY: 33423

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.454

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.637

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: 0.721 AC: 80210 AN: 111282 Hom.: 20364 Cov.: 24 AF XY: 0.723 AC XY: 24216 AN XY: 33486

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.629

Alfa AF: 0.743 Hom.: 8949

Bravo AF: 0.699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912956; hg19: chrX-57010138;