rs1809231

Variant names:

• chr2-218397456-G-C
• rs1809231
• NM_001400273.1:c.16+208G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-218397456-G-C
• chr2-218397456-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CTDSP1	NM_001400273.1	c.16+208G>C		intron_variant	Intron 1 of 6		NP_001387202.1
CTDSP1	NR_174456.1	n.164+942G>C		intron_variant	Intron 1 of 6
CTDSP1	NR_174457.1	n.164+942G>C		intron_variant	Intron 1 of 6
CTDSP1	NR_174458.1	n.141+288G>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTDSP1	ENST00000710828.1	c.-354+208G>C		intron_variant	Intron 1 of 6			ENSP00000518506.1

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

African (AFR) AF: 0.755 AC: 31285 AN: 41452

American (AMR) AF: 0.460 AC: 7024 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3464

East Asian (EAS) AF: 0.266 AC: 1371 AN: 5154

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4820

European-Finnish (FIN) AF: 0.383 AC: 4039 AN: 10548

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28941 AN: 67958

Other (OTH) AF: 0.486 AC: 1025 AN: 2108

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1809231; hg19: chr2-219262179;