rs13258200

chr8-144405804-A-C

Variant summary

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

The NM_013291.3(CPSF1):c.144+3211T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,930 control chromosomes in the GnomAD database, including 11,604 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 0.38 (11604 hom., cov: 31)
• Consequence: CPSF1 NM_013291.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

Genes affected

CPSF1 (HGNC:2324): (cleavage and polyadenylation specific factor 1) Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleavage and poly(A) synthesis. CPSF1 is the largest subunit of the CPSF complex (Murthy and Manley, 1995 [PubMed 7590244]).[supplied by OMIM, Mar 2008]

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 (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPSF1	NM_013291.3	c.144+3211T>G		intron_variant		ENST00000616140.2
CPSF1	XM_006716548.3	c.144+3211T>G		intron_variant
CPSF1	XM_047421733.1	c.-104+26T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPSF1	ENST00000616140.2	c.144+3211T>G		intron_variant		1	NM_013291.3	P1
CPSF1	ENST00000620219.4	c.144+3211T>G		intron_variant		1		P1
CPSF1	ENST00000531042.5	c.144+3211T>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58108 AN: 151814 Hom.: 11596 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.383 AC: 58148 AN: 151930 Hom.: 11604 Cov.: 31 AF XY: 0.389 AC XY: 28887 AN XY: 74288

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.380

Alfa AF: 0.370 Hom.: 5518

Bravo AF: 0.389

Asia WGS AF: 0.570 AC: 1980 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	4.0
Dann	Benign	0.87

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: rs13258200; hg19: chr8-145631197;