NM_001275.4:c.856G>A

Variant names:

• chr14-92932417-G-A
• rs1465378809
• NM_001275.4:c.856G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001275.4(CHGA):​c.856G>A​(p.Glu286Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000702 in 1,423,800 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: 7.0e-7 (0 hom.)
• Consequence: CHGA NM_001275.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.55

Genes affected

CHGA (HGNC:1929): (chromogranin A) The protein encoded by this gene is a member of the chromogranin/secretogranin family of neuroendocrine secretory proteins. It is found in secretory vesicles of neurons and endocrine cells. This gene product is a precursor to three biologically active peptides; vasostatin, pancreastatin, and parastatin. These peptides act as autocrine or paracrine negative modulators of the neuroendocrine system. Two other peptides, catestatin and chromofungin, have antimicrobial activity and antifungal activity, respectively. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1178481).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHGA	NM_001275.4	c.856G>A	p.Glu286Lys	missense_variant	Exon 7 of 8	ENST00000216492.10	NP_001266.1
CHGA	NM_001301690.2	c.403G>A	p.Glu135Lys	missense_variant	Exon 6 of 7		NP_001288619.1
CHGA	XM_011536370.3	c.856G>A	p.Glu286Lys	missense_variant	Exon 8 of 9		XP_011534672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHGA	ENST00000216492.10	c.856G>A	p.Glu286Lys	missense_variant	Exon 7 of 8	1	NM_001275.4	ENSP00000216492.5
CHGA	ENST00000334654.4	c.403G>A	p.Glu135Lys	missense_variant	Exon 6 of 7	1		ENSP00000334023.4
CHGA	ENST00000556876.1	n.74G>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
CHGA	ENST00000553866.1	n.*149G>A		downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.02e-7 AC: 1 AN: 1423800 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 704294

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000260

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.14	T;T
Eigen	Benign	-0.58
Eigen_PC	Benign	-0.55
FATHMM_MKL	Benign	0.41	N
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.12	T;T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	1.8	L;.
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-1.6	N;N
REVEL	Benign	0.018
Sift	Benign	0.12	T;T
Sift4G	Benign	0.10	T;T
Polyphen		0.16	B;B
Vest4		0.12
MutPred		0.38		Gain of ubiquitination at E286 (P = 0.0011);.;
MVP		0.30
MPC		0.35
ClinPred		0.41	T
GERP RS		3.0
Varity_R		0.061
gMVP		0.21

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

LitVar

Other links and lift over

dbSNP: rs1465378809; hg19: chr14-93398762;