16-30903305-T-C

Variant names:

• chr16-30903305-T-C
• rs1046276
• NM_001330.5:c.*766T>C

Variant summary

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

The NM_001330.5(CTF1):​c.*766T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 153,024 control chromosomes in the GnomAD database, including 29,789 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 0.62 (29557 hom., cov: 30)
  • Exomes 𝑓: 0.59 (232 hom.)
• Consequence: CTF1 NM_001330.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTF1	NM_001330.5	c.*766T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000279804.3	NP_001321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTF1	ENST00000279804.3	c.*766T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_001330.5	ENSP00000279804.2
CTF1	ENST00000395019.3	c.*766T>C		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000378465.3

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93705 AN: 151686 Hom.: 29538 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.658

GnomAD4 exome AF: 0.591 AC: 721 AN: 1220 Hom.: 232 Cov.: 0 AF XY: 0.578 AC XY: 517 AN XY: 894

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.611

Gnomad4 ASJ exome AF: 0.600

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.583

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.636

GnomAD4 genome AF: 0.618 AC: 93768 AN: 151804 Hom.: 29557 Cov.: 30 AF XY: 0.615 AC XY: 45580 AN XY: 74158

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.654

Alfa AF: 0.647 Hom.: 28776

Bravo AF: 0.620

Asia WGS AF: 0.572 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.56

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: rs1046276; hg19: chr16-30914626;