1-114717147-T-C

Variant names:

• chr1-114717147-T-C
• rs1065634
• NM_001007553.3:c.*1022A>G

Variant summary

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

The NM_001007553.3(CSDE1):​c.*1022A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 152,628 control chromosomes in the GnomAD database, including 227 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 0.050 (227 hom., cov: 33)
  • Exomes 𝑓: 0.043 (0 hom.)
• Consequence: CSDE1 NM_001007553.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 13 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.069 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.*1022A>G		3_prime_UTR	Exon 20 of 20	NP_001007554.1
	CSDE1	NM_001242891.2		c.*1022A>G		3_prime_UTR	Exon 21 of 21	NP_001229820.1
	CSDE1	NM_001130523.3		c.*1022A>G		3_prime_UTR	Exon 20 of 20	NP_001123995.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSDE1	ENST00000358528.9	TSL:1 MANE Select	c.*1022A>G		3_prime_UTR	Exon 20 of 20	ENSP00000351329.4
	CSDE1	ENST00000438362.7	TSL:1	c.*1022A>G		3_prime_UTR	Exon 21 of 21	ENSP00000407724.3
	CSDE1	ENST00000339438.10	TSL:1	c.*1022A>G		3_prime_UTR	Exon 19 of 19	ENSP00000342408.6

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7657 AN: 152072 Hom.: 228 Cov.: 33

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0750

GnomAD4 exome AF: 0.0434 AC: 19 AN: 438 Hom.: 0 Cov.: 0 AF XY: 0.0464 AC XY: 13 AN XY: 280

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0306 AC: 12 AN: 392

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.206 AC: 7 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.0503 AC: 7654 AN: 152190 Hom.: 227 Cov.: 33 AF XY: 0.0487 AC XY: 3624 AN XY: 74412

African (AFR) AF: 0.0179 AC: 742 AN: 41518

American (AMR) AF: 0.0502 AC: 767 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3470

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5172

South Asian (SAS) AF: 0.0527 AC: 254 AN: 4824

European-Finnish (FIN) AF: 0.0431 AC: 456 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0706 AC: 4803 AN: 68000

Other (OTH) AF: 0.0747 AC: 158 AN: 2116

Alfa AF: 0.0635 Hom.: 947

Bravo AF: 0.0498

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.032
PromoterAI		0.022	Neutral
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: rs1065634; hg19: chr1-115259768;