20-56396330-G-T

Variant names:

• chr20-56396330-G-T
• rs6064391
• NM_001324.3:c.169+609G>T

Variant summary

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

The NM_001324.3(CSTF1):​c.169+609G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,118 control chromosomes in the GnomAD database, including 16,558 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 0.45 (16558 hom., cov: 33)
• Consequence: CSTF1 NM_001324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 5 publications found

Genes affected

CSTF1 (HGNC:2483): (cleavage stimulation factor subunit 1) This gene encodes one of three subunits which combine to form cleavage stimulation factor (CSTF). CSTF is involved in the polyadenylation and 3'end cleavage of pre-mRNAs. Similar to mammalian G protein beta subunits, this protein contains transducin-like repeats. Several transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSTF1	NM_001324.3	c.169+609G>T		intron_variant	Intron 2 of 5	ENST00000217109.9	NP_001315.1
CSTF1	NM_001033521.2	c.169+609G>T		intron_variant	Intron 2 of 5		NP_001028693.1
CSTF1	NM_001033522.2	c.169+609G>T		intron_variant	Intron 2 of 5		NP_001028694.1
CSTF1	XM_011528600.2	c.169+609G>T		intron_variant	Intron 2 of 5		XP_011526902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSTF1	ENST00000217109.9	c.169+609G>T		intron_variant	Intron 2 of 5	1	NM_001324.3	ENSP00000217109.4

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68213 AN: 152000 Hom.: 16564 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.448 AC: 68215 AN: 152118 Hom.: 16558 Cov.: 33 AF XY: 0.452 AC XY: 33643 AN XY: 74362

African (AFR) AF: 0.272 AC: 11277 AN: 41516

American (AMR) AF: 0.511 AC: 7806 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4385 AN: 5188

South Asian (SAS) AF: 0.494 AC: 2387 AN: 4828

European-Finnish (FIN) AF: 0.549 AC: 5788 AN: 10538

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33528 AN: 67986

Other (OTH) AF: 0.451 AC: 951 AN: 2110

Alfa AF: 0.473 Hom.: 6366

Bravo AF: 0.443

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.70
PhyloP100		-0.59
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: rs6064391; hg19: chr20-54971386;