11-63825149-C-T

Variant names:

• chr11-63825149-C-T
• rs10897449
• NM_138471.3:c.935-1779C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138471.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPINDOC	NM_138471.3	MANE Select	c.935-1779C>T		intron	N/A	NP_612480.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPINDOC	ENST00000294244.9	TSL:1 MANE Select	c.935-1779C>T		intron	N/A	ENSP00000294244.3

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

African (AFR) AF: 0.135 AC: 5590 AN: 41478

American (AMR) AF: 0.295 AC: 4509 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3472

East Asian (EAS) AF: 0.175 AC: 903 AN: 5174

South Asian (SAS) AF: 0.606 AC: 2915 AN: 4810

European-Finnish (FIN) AF: 0.485 AC: 5117 AN: 10558

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31112 AN: 67944

Other (OTH) AF: 0.362 AC: 765 AN: 2112

Alfa AF: 0.420 Hom.: 53875

Bravo AF: 0.319

Asia WGS AF: 0.344 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10897449; hg19: chr11-63592621;