rs10489525

Variant names:

• chr1-114721064-G-A
• rs10489525
• NM_001007553.3:c.1874-347C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-114721064-G-A
• chr1-114721064-G-C

Variant summary

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

The NM_001007553.3(CSDE1):​c.1874-347C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,030 control chromosomes in the GnomAD database, including 8,086 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 0.32 (8086 hom., cov: 32)
• Consequence: CSDE1 NM_001007553.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 17 publications found

Genes affected

CSDE1 (HGNC:29905): (cold shock domain containing E1) Enables RNA stem-loop binding activity. Involved in IRES-dependent viral translational initiation; nuclear-transcribed mRNA catabolic process, no-go decay; and stress granule assembly. Located in Golgi apparatus; cytosol; and plasma membrane. Part of CRD-mediated mRNA stability complex. [provided by Alliance of Genome Resources, Apr 2022]

CSDE1 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007553.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSDE1	NM_001007553.3	MANE Select	c.1874-347C>T		intron	N/A	NP_001007554.1
	CSDE1	NM_001242891.2		c.2012-347C>T		intron	N/A	NP_001229820.1
	CSDE1	NM_001130523.3		c.1919-347C>T		intron	N/A	NP_001123995.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSDE1	ENST00000358528.9	TSL:1 MANE Select	c.1874-347C>T		intron	N/A	ENSP00000351329.4
	CSDE1	ENST00000369530.5	TSL:1	c.1919-347C>T		intron	N/A	ENSP00000358543.1
	CSDE1	ENST00000438362.7	TSL:1	c.1874-347C>T		intron	N/A	ENSP00000407724.3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48757 AN: 151912 Hom.: 8080 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.321 AC: 48803 AN: 152030 Hom.: 8086 Cov.: 32 AF XY: 0.326 AC XY: 24248 AN XY: 74314

African (AFR) AF: 0.355 AC: 14700 AN: 41446

American (AMR) AF: 0.369 AC: 5634 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2069 AN: 5170

South Asian (SAS) AF: 0.477 AC: 2297 AN: 4820

European-Finnish (FIN) AF: 0.329 AC: 3474 AN: 10562

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18789 AN: 67976

Other (OTH) AF: 0.320 AC: 673 AN: 2106

Alfa AF: 0.290 Hom.: 14277

Bravo AF: 0.325

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.58
PhyloP100		-0.57
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: rs10489525; hg19: chr1-115263685;