11-63825149-C-T

Variant summary

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

The NM_138471.3(SPINDOC):c.935-1779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,026 control chromosomes in the GnomAD database, including 11,196 homozygotes. 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 0.35 (11196 hom., cov: 31)
• Consequence: SPINDOC NM_138471.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

SPINDOC (HGNC:25115): (spindlin interactor and repressor of chromatin binding) Involved in negative regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPINDOC	NM_138471.3	c.935-1779C>T		intron_variant		ENST00000294244.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPINDOC	ENST00000294244.9	c.935-1779C>T		intron_variant		1	NM_138471.3	P1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53449 AN: 151906 Hom.: 11201 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.352 AC: 53440 AN: 152026 Hom.: 11196 Cov.: 31 AF XY: 0.355 AC XY: 26387 AN XY: 74310

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.362

Alfa AF: 0.437 Hom.: 24850

Bravo AF: 0.319

Asia WGS AF: 0.344 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.0
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10897449; hg19: chr11-63592621;