rs797045046

Positions:

• chr20-58891760-C-G
• chr20-58891760-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1 PM2 PP2 BP4

The NM_000516.7(GNAS):​c.34C>G​(p.Gln12Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000898 in 1,113,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/16 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: 28)
  • Exomes 𝑓: 9.0e-7 (0 hom.)
• Consequence: GNAS NM_000516.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79

Genes affected

GNAS (HGNC:4392): (GNAS complex locus) This locus has a highly complex imprinted expression pattern. It gives rise to maternally, paternally, and biallelically expressed transcripts that are derived from four alternative promoters and 5' exons. Some transcripts contain a differentially methylated region (DMR) at their 5' exons, and this DMR is commonly found in imprinted genes and correlates with transcript expression. An antisense transcript is produced from an overlapping locus on the opposite strand. One of the transcripts produced from this locus, and the antisense transcript, are paternally expressed noncoding RNAs, and may regulate imprinting in this region. In addition, one of the transcripts contains a second overlapping ORF, which encodes a structurally unrelated protein - Alex. Alternative splicing of downstream exons is also observed, which results in different forms of the stimulatory G-protein alpha subunit, a key element of the classical signal transduction pathway linking receptor-ligand interactions with the activation of adenylyl cyclase and a variety of cellular reponses. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene result in pseudohypoparathyroidism type 1a, pseudohypoparathyroidism type 1b, Albright hereditary osteodystrophy, pseudopseudohypoparathyroidism, McCune-Albright syndrome, progressive osseus heteroplasia, polyostotic fibrous dysplasia of bone, and some pituitary tumors. [provided by RefSeq, Aug 2012]

GNAS (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a signal_peptide (size 45) in uniprot entity GNAS3_HUMAN there are 10 pathogenic changes around while only 0 benign (100%) in NM_000516.7
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), GNAS. . Gene score misZ 2.6546 (greater than the threshold 3.09). Trascript score misZ 4.8361 (greater than threshold 3.09). GenCC has associacion of gene with ACTH-independent macronodular adrenal hyperplasia 1, pseudohypoparathyroidism type 1B, pseudohypoparathyroidism type 1C, pseudohypoparathyroidism type 1A, progressive osseous heteroplasia, pseudopseudohypoparathyroidism, McCune-Albright syndrome.
• BP4: Computational evidence support a benign effect (MetaRNN=0.2930197).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAS	NM_000516.7	c.34C>G	p.Gln12Glu	missense_variant	1/13	ENST00000371085.8	NP_000507.1
GNAS	NM_016592.5	c.*43-3852C>G		intron_variant		ENST00000371075.7	NP_057676.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAS	ENST00000371085.8	c.34C>G	p.Gln12Glu	missense_variant	1/13	1	NM_000516.7	ENSP00000360126.3
GNAS	ENST00000354359.12	c.34C>G	p.Gln12Glu	missense_variant	1/13	1		ENSP00000346328.7
GNAS	ENST00000371095.7	c.34C>G	p.Gln12Glu	missense_variant	1/12	1		ENSP00000360136.3
GNAS	ENST00000371075.7	c.*43-3852C>G		intron_variant		1	NM_016592.5	ENSP00000360115.3
GNAS	ENST00000676826.2	c.2069-3852C>G		intron_variant				ENSP00000504675.2
GNAS	ENST00000371102.8	c.2069-3852C>G		intron_variant		5		ENSP00000360143.4
GNAS	ENST00000470512.6	c.-39+2407C>G		intron_variant		5		ENSP00000499552.2
GNAS	ENST00000480232.6	c.-39+2211C>G		intron_variant		5		ENSP00000499545.2
GNAS	ENST00000663479.2	c.-38-3852C>G		intron_variant				ENSP00000499353.2
GNAS	ENST00000462499.6	c.-38-3852C>G		intron_variant		2		ENSP00000499758.2
GNAS	ENST00000467227.6	c.-38-3852C>G		intron_variant		3		ENSP00000499681.2
GNAS	ENST00000478585.6	c.-39+2407C>G		intron_variant		2		ENSP00000499762.2
GNAS	ENST00000481039.6	c.-39+2852C>G		intron_variant		5		ENSP00000499767.2
GNAS	ENST00000485673.6	c.-39+2211C>G		intron_variant		5		ENSP00000499334.2
GNAS	ENST00000488546.6	c.-39+2942C>G		intron_variant		5		ENSP00000499332.2
GNAS	ENST00000461152.6	c.*51+971C>G		intron_variant		5		ENSP00000499274.1
GNAS	ENST00000453292.7	c.*43-3852C>G		intron_variant		5		ENSP00000392000.2

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD3 exomes AF: 0.00000502 AC: 1 AN: 199320 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 110588

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000360

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 8.98e-7 AC: 1 AN: 1113852 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 551478

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000328

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	0.0052	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	21
DANN	Benign	0.94
DEOGEN2	Benign	0.24	.;T;.;.;T;T;T
Eigen	Benign	-0.56
Eigen_PC	Benign	-0.42
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Uncertain	0.91	D;D;D;D;D;D;D
M_CAP	Pathogenic	0.52	D
MetaRNN	Benign	0.15	T;T;T;T;T;T;T
MetaSVM	Benign	-0.57	T
MutationAssessor	Benign	-0.23	N;N;N;N;.;.;.
PROVEAN	Benign	-0.55	N;N;N;N;N;N;N
REVEL	Benign	0.24
Sift	Benign	0.78	T;T;T;T;T;T;T
Sift4G	Benign	0.56	T;T;T;T;T;T;T
Polyphen		0.0	.;B;.;B;.;.;.
Vest4		0.20
MutPred		0.31		Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);Loss of MoRF binding (P = 0.0708);.;
MVP		0.38
ClinPred		0.064	T
GERP RS		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs797045046; hg19: chr20-57466815;