16-30898385-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001330.5(CTF1):c.26-1030C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,918 control chromosomes in the GnomAD database, including 5,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (5201 hom., cov: 31)
• Consequence: CTF1 NM_001330.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.274

Genes affected

CTF1 (HGNC:2499): (cardiotrophin 1) The protein encoded by this gene is a secreted cytokine that induces cardiac myocyte hypertrophy in vitro. It has been shown to bind and activate the ILST/gp130 receoptor. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 16-30898385-C-G is Benign according to our data. Variant chr16-30898385-C-G is described in ClinVar as [Benign]. Clinvar id is 1164131.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTF1	NM_001330.5	c.26-1030C>G		intron_variant		ENST00000279804.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTF1	ENST00000279804.3	c.26-1030C>G		intron_variant		1	NM_001330.5	P3
CTF1	ENST00000395019.3	c.26-1033C>G		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37248 AN: 151800 Hom.: 5205 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.245 AC: 37245 AN: 151918 Hom.: 5201 Cov.: 31 AF XY: 0.251 AC XY: 18630 AN XY: 74220

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0860

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.246

Alfa AF: 0.162 Hom.: 333

Bravo AF: 0.225

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Dilated Cardiomyopathy, Dominant Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.24

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: rs11862962; hg19: chr16-30909706;