Variant 12-57824599-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_005730.4(CTDSP2):c.412-280C>T variant causes a intron change. The variant allele was found at a frequency of 0.0146 in 620,694 control chromosomes in the GnomAD database, including 99 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 0.012 ( 9 hom., cov: 32)

Exomes 𝑓: 0.016 ( 90 hom. )

Consequence

CTDSP2
NM_005730.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.00

Variant links:

Genes affected

CTDSP2 (HGNC:17077): (CTD small phosphatase 2) Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in protein dephosphorylation. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CTDSP2 links:

MIR26A2 (HGNC:31611): (microRNA 26a-2) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR26A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0115 (1756/152332) while in subpopulation SAS AF= 0.0236 (114/4824). AF 95% confidence interval is 0.0201. There are 9 homozygotes in gnomad4. There are 819 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CTDSP2	NM_005730.4 linkuse as main transcript	c.412-280C>T	intron_variant	ENST00000398073.7
CTDSP2	XM_005268556.3 linkuse as main transcript	c.430-280C>T	intron_variant
MIR26A2	NR_029847.1 linkuse as main transcript		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTDSP2	ENST00000398073.7 linkuse as main transcript	c.412-280C>T		intron_variant		1	NM_005730.4	P1
MIR26A2	ENST00000385054.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0115

AC:

1752

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00251

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0135

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.0202

Gnomad SAS

AF:

0.0234

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0153

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.0153

AC:

3797

AN:

247932

Hom.:

AF XY:

0.0161

AC XY:

2155

AN XY:

134200

show subpopulations

Gnomad AFR exome

AF:

0.00233

Gnomad AMR exome

AF:

0.00909

Gnomad ASJ exome

AF:

0.0280

Gnomad EAS exome

AF:

0.0219

Gnomad SAS exome

AF:

0.0223

Gnomad FIN exome

AF:

0.00749

Gnomad NFE exome

AF:

0.0163

Gnomad OTH exome

AF:

0.0186

GnomAD4 exome

AF:

0.0156

AC:

7326

AN:

468362

Hom.:

Cov.:

AF XY:

0.0162

AC XY:

4227

AN XY:

260570

show subpopulations

Gnomad4 AFR exome

AF:

0.00241

Gnomad4 AMR exome

AF:

0.00932

Gnomad4 ASJ exome

AF:

0.0291

Gnomad4 EAS exome

AF:

0.0195

Gnomad4 SAS exome

AF:

0.0207

Gnomad4 FIN exome

AF:

0.00755

Gnomad4 NFE exome

AF:

0.0158

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.0115

AC:

1756

AN:

152332

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

819

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00250

Gnomad4 AMR

AF:

0.0135

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.0202

Gnomad4 SAS

AF:

0.0236

Gnomad4 FIN

AF:

0.00480

Gnomad4 NFE

AF:

0.0153

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0156

Hom.:

Bravo

AF:

0.0123

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over