X-56983705-C-T

Variant names:

• chrX-56983705-C-T
• rs912956
• ENST00000478405.1:n.*204+561G>A

Variant summary

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

The ENST00000639257.1(SPIN3):​n.*204+561G>A 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 0.72 (20364 hom., 24216 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: SPIN3 ENST00000639257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 4 publications found

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

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639257.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPIN3	NR_027139.2		n.766+561G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPIN3	ENST00000478405.1	TSL:1	n.*204+561G>A		intron	N/A	ENSP00000433337.1	Q5JUX0-2
	SPIN3	ENST00000639257.1	TSL:3	n.*204+561G>A		intron	N/A	ENSP00000492259.1	Q5JUX0-2
	SPIN3	ENST00000640131.1	TSL:1	n.*204+561G>A		intron	N/A	ENSP00000491666.1	Q5JUX0-2

Frequencies

GnomAD3 genomes AF: 0.721 AC: 80174 AN: 111227 Hom.: 20368 Cov.: 24

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

African (AFR) AF: 0.673 AC: 20623 AN: 30628

American (AMR) AF: 0.627 AC: 6604 AN: 10526

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1480 AN: 2637

East Asian (EAS) AF: 0.657 AC: 2294 AN: 3490

South Asian (SAS) AF: 0.670 AC: 1764 AN: 2634

European-Finnish (FIN) AF: 0.846 AC: 5028 AN: 5944

Middle Eastern (MID) AF: 0.459 AC: 100 AN: 218

European-Non Finnish (NFE) AF: 0.769 AC: 40746 AN: 53001

Other (OTH) AF: 0.629 AC: 956 AN: 1521

Alfa AF: 0.743 Hom.: 8949

Bravo AF: 0.699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.39
PhyloP100		0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs912956;

hg19: chrX-57010138;