NM_001003699.4:c.87G>C

Variant names:

• chr6-7181998-G-C
• NM_001003699.4:c.87G>C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_001003699.4(RREB1):​c.87G>C​(p.Lys29Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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: 32)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: RREB1 NM_001003699.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09

Genes affected

RREB1 (HGNC:10449): (ras responsive element binding protein 1) The protein encoded by this gene is a zinc finger transcription factor that binds to RAS-responsive elements (RREs) of gene promoters. It has been shown that the calcitonin gene promoter contains an RRE and that the encoded protein binds there and increases expression of calcitonin, which may be involved in Ras/Raf-mediated cell differentiation. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08782151).
• BS2: High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RREB1	NM_001003699.4	c.87G>C	p.Lys29Asn	missense_variant	Exon 4 of 13	ENST00000379938.7	NP_001003699.1
RREB1	NM_001003698.4	c.87G>C	p.Lys29Asn	missense_variant	Exon 4 of 12		NP_001003698.1
RREB1	NM_001168344.2	c.87G>C	p.Lys29Asn	missense_variant	Exon 4 of 12		NP_001161816.1
RREB1	NM_001003700.2	c.87G>C	p.Lys29Asn	missense_variant	Exon 4 of 12		NP_001003700.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RREB1	ENST00000379938.7	c.87G>C	p.Lys29Asn	missense_variant	Exon 4 of 13	1	NM_001003699.4	ENSP00000369270.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000410 AC: 6 AN: 1461870 Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4 AN XY: 727242

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Uncertain	0.99
DEOGEN2	Benign	0.016	T;T;.;.;.;T;T
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.21
FATHMM_MKL	Benign	0.74	D
LIST_S2	Benign	0.72	.;T;T;T;T;T;T
M_CAP	Benign	0.0071	T
MetaRNN	Benign	0.088	T;T;T;T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.67	N;.;N;.;N;N;.
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.96	N;N;N;N;N;N;N
REVEL	Benign	0.029
Sift	Benign	0.21	T;T;T;T;T;T;T
Sift4G	Uncertain	0.055	T;T;T;T;T;T;T
Polyphen		0.0040	B;.;B;.;B;B;.
Vest4		0.32
MutPred		0.26		Loss of ubiquitination at K29 (P = 0.0037);Loss of ubiquitination at K29 (P = 0.0037);Loss of ubiquitination at K29 (P = 0.0037);Loss of ubiquitination at K29 (P = 0.0037);Loss of ubiquitination at K29 (P = 0.0037);Loss of ubiquitination at K29 (P = 0.0037);Loss of ubiquitination at K29 (P = 0.0037);
MVP		0.32
MPC		0.62
ClinPred		0.097	T
GERP RS		3.0
Varity_R		0.041
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-7182231;