6-139373365-CGCCGCT-CGCCGCTGCCGCT

Variant names:

• chr6-139373365-C-CGCCGCT
• rs751501072
• NM_006079.5:c.574_579dupAGCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006079.5(CITED2):​c.574_579dupAGCGGC​(p.Gly193_Gly194insSerGly) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CITED2 NM_006079.5 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

CITED2 (HGNC:1987): (Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2) The protein encoded by this gene inhibits transactivation of HIF1A-induced genes by competing with binding of hypoxia-inducible factor 1-alpha to p300-CH1. Mutations in this gene are a cause of cardiac septal defects. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CITED2	NM_006079.5	c.574_579dupAGCGGC	p.Gly193_Gly194insSerGly	conservative_inframe_insertion	Exon 2 of 2	ENST00000367651.4	NP_006070.2
CITED2	NM_001168389.3	c.589_594dupAGCGGC	p.Gly198_Gly199insSerGly	conservative_inframe_insertion	Exon 2 of 2		NP_001161861.2
CITED2	NM_001168388.3	c.574_579dupAGCGGC	p.Gly193_Gly194insSerGly	conservative_inframe_insertion	Exon 2 of 2		NP_001161860.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CITED2	ENST00000367651.4	c.574_579dupAGCGGC	p.Gly193_Gly194insSerGly	conservative_inframe_insertion	Exon 2 of 2	1	NM_006079.5	ENSP00000356623.2
CITED2	ENST00000537332.2	c.589_594dupAGCGGC	p.Gly198_Gly199insSerGly	conservative_inframe_insertion	Exon 2 of 2	3		ENSP00000444198.2
CITED2	ENST00000536159.2	c.574_579dupAGCGGC	p.Gly193_Gly194insSerGly	conservative_inframe_insertion	Exon 2 of 2	3		ENSP00000442831.1
ENSG00000226571	ENST00000650173.1	n.510-55714_510-55709dupCCGCTG		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751501072; hg19: chr6-139694502;