11-61429988-GC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000394888.8(CPSF7):c.-131del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.85 (54894 hom., cov: 0)
  • Exomes 𝑓: 0.86 (389320 hom.)
• Consequence: CPSF7 ENST00000394888.8 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.87

Genes affected

CPSF7 (HGNC:30098): (cleavage and polyadenylation specific factor 7) Cleavage factor Im (CFIm) is one of six factors necessary for correct cleavage and polyadenylation of pre-mRNAs. CFIm is composed of three different subunits of 25, 59, and 68 kDa, and it functions as a heterotetramer, with a dimer of the 25 kDa subunit binding to two of the 59 or 68 kDa subunits. The protein encoded by this gene represents the 59 kDa subunit, which can interact with the splicing factor U2 snRNP Auxiliary Factor (U2AF) 65 to link the splicing and polyadenylation complexes. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-61429988-GC-G is Benign according to our data. Variant chr11-61429988-GC-G is described in ClinVar as [Benign]. Clinvar id is 1266254.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPSF7	NM_001142565.3			upstream_gene_variant		ENST00000439958.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPSF7	ENST00000439958.8			upstream_gene_variant		1	NM_001142565.3	P4

Frequencies

GnomAD3 genomes AF: 0.849 AC: 128989 AN: 152002 Hom.: 54871 Cov.: 0

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.898

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.864

GnomAD4 exome AF: 0.861 AC: 900947 AN: 1046462 Hom.: 389320 Cov.: 0 AF XY: 0.862 AC XY: 451422 AN XY: 523876

Gnomad4 AFR exome AF: 0.775

Gnomad4 AMR exome AF: 0.885

Gnomad4 ASJ exome AF: 0.892

Gnomad4 EAS exome AF: 0.974

Gnomad4 SAS exome AF: 0.868

Gnomad4 FIN exome AF: 0.884

Gnomad4 NFE exome AF: 0.855

Gnomad4 OTH exome AF: 0.870

GnomAD4 genome AF: 0.848 AC: 129060 AN: 152116 Hom.: 54894 Cov.: 0 AF XY: 0.852 AC XY: 63368 AN XY: 74388

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.858

Bravo AF: 0.843

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs34378918; hg19: chr11-61197460;