rs10489525

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSDE1	NM_001007553.3	c.1874-347C>T		intron_variant		ENST00000358528.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSDE1	ENST00000358528.9	c.1874-347C>T		intron_variant		1	NM_001007553.3	P1

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

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.320

Alfa AF: 0.286 Hom.: 9377

Bravo AF: 0.325

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.58

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: rs10489525; hg19: chr1-115263685;