6-139373363-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_006079.5(CITED2):c.582C>T(p.Gly194=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00373 in 1,582,560 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0024 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0039 (14 hom.)
• Consequence: CITED2 NM_006079.5 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.951

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP6: Variant 6-139373363-G-A is Benign according to our data. Variant chr6-139373363-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 717442.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-139373363-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=0.951 with no splicing effect.
• BS2: High AC in GnomAd at 367 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CITED2	NM_006079.5	c.582C>T	p.Gly194=	synonymous_variant	2/2	ENST00000367651.4
CITED2	NM_001168389.3	c.597C>T	p.Gly199=	synonymous_variant	2/2
CITED2	NM_001168388.3	c.582C>T	p.Gly194=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CITED2	ENST00000367651.4	c.582C>T	p.Gly194=	synonymous_variant	2/2	1	NM_006079.5	P1
	ENST00000650173.1	n.510-55718G>A		intron_variant, non_coding_transcript_variant
CITED2	ENST00000537332.2	c.597C>T	p.Gly199=	synonymous_variant	2/2	3
CITED2	ENST00000536159.2	c.582C>T	p.Gly194=	synonymous_variant	2/2	3		P1

Frequencies

GnomAD3 genomes AF: 0.00242 AC: 367 AN: 151580 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000750

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00322

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000473

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00404

Gnomad OTH AF: 0.00336

GnomAD3 exomes AF: 0.00221 AC: 473 AN: 214128 Hom.: 1 AF XY: 0.00208 AC XY: 249 AN XY: 119770

Gnomad AFR exome AF: 0.000643

Gnomad AMR exome AF: 0.00260

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000737

Gnomad FIN exome AF: 0.000945

Gnomad NFE exome AF: 0.00355

Gnomad OTH exome AF: 0.00195

GnomAD4 exome AF: 0.00387 AC: 5536 AN: 1430872 Hom.: 14 Cov.: 31 AF XY: 0.00379 AC XY: 2701 AN XY: 712070

Gnomad4 AFR exome AF: 0.000568

Gnomad4 AMR exome AF: 0.00240

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000678

Gnomad4 FIN exome AF: 0.000657

Gnomad4 NFE exome AF: 0.00467

Gnomad4 OTH exome AF: 0.00359

GnomAD4 genome AF: 0.00242 AC: 367 AN: 151688 Hom.: 2 Cov.: 32 AF XY: 0.00237 AC XY: 176 AN XY: 74198

Gnomad4 AFR AF: 0.000747

Gnomad4 AMR AF: 0.00321

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.000473

Gnomad4 NFE AF: 0.00404

Gnomad4 OTH AF: 0.00333

Alfa AF: 0.000923 Hom.: 0

Bravo AF: 0.00254

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Dec 31, 2019	- -

CITED2-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 03, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	7.0
Dann	Benign	0.93

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: rs530008417; hg19: chr6-139694500;