2-218397456-G-C

Position:

• chr2-218397456-G-C

Variant summary

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

The NM_001400273.1(CTDSP1):​c.16+208G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,970 control chromosomes in the GnomAD database, including 21,345 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 0.51 (21345 hom., cov: 31)
• Consequence: CTDSP1 NM_001400273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

CTDSP1 (HGNC:21614): (CTD small phosphatase 1) This gene encodes a member of the small C-terminal domain phosphatase (SCP) family of nuclear phosphatases. These proteins play a role in transcriptional regulation through specific dephosphorylation of phosphoserine 5 within tandem heptapeptide repeats of the C-terminal domain of RNA polymerase II. The encoded protein plays a role in neuronal gene silencing in non-neuronal cells, and may also inhibit osteoblast differentiation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTDSP1	NM_001400273.1	c.16+208G>C		intron_variant			NP_001387202.1
CTDSP1	NR_174456.1	n.164+942G>C		intron_variant, non_coding_transcript_variant
CTDSP1	NR_174457.1	n.164+942G>C		intron_variant, non_coding_transcript_variant
CTDSP1	NR_174458.1	n.141+288G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTDSP1	ENST00000710828.1	c.-354+208G>C		intron_variant				ENSP00000518506

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76746 AN: 151852 Hom.: 21299 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.506 AC: 76863 AN: 151970 Hom.: 21345 Cov.: 31 AF XY: 0.498 AC XY: 36980 AN XY: 74256

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.486

Alfa AF: 0.300 Hom.: 720

Bravo AF: 0.522

Asia WGS AF: 0.329 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1809231; hg19: chr2-219262179;