NM_001377190.1:c.-369A>T

Variant names:

• chr4-1249829-T-A
• rs3755920
• NM_001377190.1:c.-369A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001377190.1(CTBP1):​c.-369A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CTBP1 NM_001377190.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 20 publications found

Genes affected

CTBP1 (HGNC:2494): (C-terminal binding protein 1) This gene encodes a protein that binds to the C-terminus of adenovirus E1A proteins. This phosphoprotein is a transcriptional repressor and may play a role during cellular proliferation. This protein and the product of a second closely related gene, CTBP2, can dimerize. Both proteins can also interact with a polycomb group protein complex which participates in regulation of gene expression during development. Alternative splicing of transcripts from this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

CTBP1-DT (HGNC:28307): (CTBP1 divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTBP1	NM_001377190.1		c.-369A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 10	NP_001364119.1
	CTBP1	NM_001377193.1		c.-369A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 10	NP_001364122.1
	CTBP1	NM_001377190.1		c.-369A>T		5_prime_UTR	Exon 1 of 10	NP_001364119.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTBP1	ENST00000506180.5	TSL:5	c.-198A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 5	ENSP00000424684.2
	CTBP1	ENST00000515399.5	TSL:3	c.-369A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 5	ENSP00000425053.1
	CTBP1	ENST00000506180.5	TSL:5	c.-198A>T		5_prime_UTR	Exon 1 of 5	ENSP00000424684.2

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 55990 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 34978

African (AFR) AF: 0.00 AC: 0 AN: 376

American (AMR) AF: 0.00 AC: 0 AN: 734

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 978

East Asian (EAS) AF: 0.00 AC: 0 AN: 222

South Asian (SAS) AF: 0.00 AC: 0 AN: 19524

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2830

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1402

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 27848

Other (OTH) AF: 0.00 AC: 0 AN: 2076

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		-0.96
PromoterAI		0.00090	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3755920; hg19: chr4-1243617;