rs2001660

Variant names:

• chr2-9473312-T-C
• rs2001660
• NM_016207.4:c.*295T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016207.4(CPSF3):​c.*295T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,018 control chromosomes in the GnomAD database, including 27,498 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 0.58 (27498 hom., cov: 31)
• Consequence: CPSF3 NM_016207.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

Genes affected

CPSF3 (HGNC:2326): (cleavage and polyadenylation specific factor 3) This gene encodes a member of the metallo-beta-lactamase family. The encoded protein is a 73kDa subunit of the cleavage and polyadenylation specificity factor and functions as an endonuclease that recognizes the pre-mRNA 3'-cleavage site AAUAAA prior to polyadenylation. It also cleaves after the pre-mRNA sequence ACCCA during histone 3'-end pre-mRNA processing. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPSF3	NM_016207.4	c.*295T>C		downstream_gene_variant		ENST00000238112.8	NP_057291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPSF3	ENST00000238112.8	c.*295T>C		downstream_gene_variant		1	NM_016207.4	ENSP00000238112.3
CPSF3	ENST00000460593.1	c.*295T>C		downstream_gene_variant		1		ENSP00000418957.1
CPSF3	ENST00000489403.1	n.*214T>C		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88796 AN: 151898 Hom.: 27454 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.585 AC: 88890 AN: 152018 Hom.: 27498 Cov.: 31 AF XY: 0.571 AC XY: 42393 AN XY: 74278

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.600

Alfa AF: 0.589 Hom.: 12172

Bravo AF: 0.586

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001660; hg19: chr2-9613441;