rs1463335

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007007.3(CPSF6):​c.*3787T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 349,128 control chromosomes in the GnomAD database, including 56,494 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 0.55 ( 23143 hom., cov: 31)
Exomes 𝑓: 0.57 ( 33351 hom. )

Consequence

CPSF6
NM_007007.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.249
Variant links:
Genes affected
CPSF6 (HGNC:13871): (cleavage and polyadenylation specific factor 6) The protein encoded by this gene is one subunit of a cleavage factor required for 3' RNA cleavage and polyadenylation processing. The interaction of the protein with the RNA is one of the earliest steps in the assembly of the 3' end processing complex and facilitates the recruitment of other processing factors. The cleavage factor complex is composed of four polypeptides. This gene encodes the 68kD subunit. It has a domain organization reminiscent of spliceosomal proteins. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CPSF6NM_007007.3 linkuse as main transcriptc.*3787T>A 3_prime_UTR_variant 10/10 ENST00000435070.7
CPSF6NM_001300947.2 linkuse as main transcriptc.*3787T>A 3_prime_UTR_variant 11/11
CPSF6XM_005268588.4 linkuse as main transcriptc.*3787T>A 3_prime_UTR_variant 11/11
CPSF6XM_005268590.4 linkuse as main transcriptc.*3787T>A 3_prime_UTR_variant 10/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CPSF6ENST00000435070.7 linkuse as main transcriptc.*3787T>A 3_prime_UTR_variant 10/101 NM_007007.3 A1Q16630-1
CPSF6ENST00000650046.1 linkuse as main transcriptc.*6107T>A 3_prime_UTR_variant, NMD_transcript_variant 12/12

Frequencies

GnomAD3 genomes
AF:
0.550
AC:
83271
AN:
151468
Hom.:
23136
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.537
Gnomad AMI
AF:
0.516
Gnomad AMR
AF:
0.565
Gnomad ASJ
AF:
0.522
Gnomad EAS
AF:
0.727
Gnomad SAS
AF:
0.683
Gnomad FIN
AF:
0.431
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.532
GnomAD4 exome
AF:
0.573
AC:
113104
AN:
197542
Hom.:
33351
Cov.:
0
AF XY:
0.580
AC XY:
66124
AN XY:
113922
show subpopulations
Gnomad4 AFR exome
AF:
0.524
Gnomad4 AMR exome
AF:
0.594
Gnomad4 ASJ exome
AF:
0.515
Gnomad4 EAS exome
AF:
0.728
Gnomad4 SAS exome
AF:
0.673
Gnomad4 FIN exome
AF:
0.440
Gnomad4 NFE exome
AF:
0.546
Gnomad4 OTH exome
AF:
0.554
GnomAD4 genome
AF:
0.550
AC:
83315
AN:
151586
Hom.:
23143
Cov.:
31
AF XY:
0.548
AC XY:
40569
AN XY:
74082
show subpopulations
Gnomad4 AFR
AF:
0.537
Gnomad4 AMR
AF:
0.565
Gnomad4 ASJ
AF:
0.522
Gnomad4 EAS
AF:
0.727
Gnomad4 SAS
AF:
0.683
Gnomad4 FIN
AF:
0.431
Gnomad4 NFE
AF:
0.552
Gnomad4 OTH
AF:
0.531
Alfa
AF:
0.554
Hom.:
2854
Bravo
AF:
0.554
Asia WGS
AF:
0.665
AC:
2310
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
7.8
DANN
Benign
0.72
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1463335; hg19: chr12-69667075; API