3-37935926-G-T

Variant names:

• chr3-37935926-G-T
• rs9311168
• NM_001008392.2:c.80-11131G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001008392.2(CTDSPL):​c.80-11131G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,086 control chromosomes in the GnomAD database, including 8,886 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 0.30 (8886 hom., cov: 31)
• Consequence: CTDSPL NM_001008392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

Genes affected

CTDSPL (HGNC:16890): (CTD small phosphatase like) Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in protein dephosphorylation. Predicted to act upstream of or within negative regulation of G1/S transition of mitotic cell cycle and negative regulation of protein phosphorylation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000308159 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTDSPL	NM_001008392.2	c.80-11131G>T		intron_variant	Intron 1 of 7	ENST00000273179.10	NP_001008393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTDSPL	ENST00000273179.10	c.80-11131G>T		intron_variant	Intron 1 of 7	1	NM_001008392.2	ENSP00000273179.5

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46284 AN: 151968 Hom.: 8866 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.305 AC: 46345 AN: 152086 Hom.: 8886 Cov.: 31 AF XY: 0.298 AC XY: 22172 AN XY: 74344

African (AFR) AF: 0.540 AC: 22380 AN: 41446

American (AMR) AF: 0.227 AC: 3472 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3470

East Asian (EAS) AF: 0.0523 AC: 271 AN: 5184

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1613 AN: 10590

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15795 AN: 67980

Other (OTH) AF: 0.292 AC: 617 AN: 2116

Alfa AF: 0.184 Hom.: 587

Bravo AF: 0.323

Asia WGS AF: 0.174 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.50
PhyloP100		-1.2
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: rs9311168; hg19: chr3-37977417;