rs9822761

chr3-37927948-T-C

Variant summary

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

The NM_001008392.2(CTDSPL):c.80-19109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,914 control chromosomes in the GnomAD database, including 7,444 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 0.27 (7444 hom., cov: 31)
• Consequence: CTDSPL NM_001008392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTDSPL	NM_001008392.2	c.80-19109T>C		intron_variant		ENST00000273179.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTDSPL	ENST00000273179.10	c.80-19109T>C		intron_variant		1	NM_001008392.2	P4

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41699 AN: 151800 Hom.: 7427 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.275 AC: 41752 AN: 151914 Hom.: 7444 Cov.: 31 AF XY: 0.268 AC XY: 19937 AN XY: 74272

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0515

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.268

Alfa AF: 0.217 Hom.: 1985

Bravo AF: 0.294

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.71

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: rs9822761; hg19: chr3-37969439;