17-43952966-T-C

Variant names:

• chr17-43952966-T-C
• NM_001394028.1:c.284A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394028.1(PYY):​c.284A>G​(p.Asp95Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D95N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PYY NM_001394028.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.130
• Publications: 0 publications found

Genes affected

PYY (HGNC:9748): (peptide YY) This gene encodes a member of the neuropeptide Y (NPY) family of peptides. The encoded preproprotein is proteolytically processed to generate two alternative peptide products that differ in length by three amino acids. These peptides, secreted by endocrine cells in the gut, exhibit different binding affinities for each of the neuropeptide Y receptors. Binding of the encoded peptides to these receptors mediates regulation of pancreatic secretion, gut mobility and energy homeostasis. Rare variations in this gene could increase susceptibility to obesity and elevated serum levels of the encoded peptides may be associated with anorexia nervosa. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06576964).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYY	NM_001394028.1	c.284A>G	p.Asp95Gly	missense_variant	Exon 4 of 4	ENST00000692052.1	NP_001380957.1
PYY	NM_004160.6	c.284A>G	p.Asp95Gly	missense_variant	Exon 7 of 7		NP_004151.4
PYY	NM_001394029.1	c.*139A>G		3_prime_UTR_variant	Exon 3 of 3		NP_001380958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYY	ENST00000692052.1	c.284A>G	p.Asp95Gly	missense_variant	Exon 4 of 4		NM_001394028.1	ENSP00000509262.1
PYY	ENST00000360085.6	c.284A>G	p.Asp95Gly	missense_variant	Exon 7 of 7	1		ENSP00000353198.1
PYY	ENST00000592796.2	c.*139A>G		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000467310.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

May 27, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.284A>G (p.D95G) alteration is located in exon 7 (coding exon 3) of the PYY gene. This alteration results from a A to G substitution at nucleotide position 284, causing the aspartic acid (D) at amino acid position 95 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	10
DANN	Benign	0.88
DEOGEN2	Benign	0.053	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.35	T
M_CAP	Benign	0.0062	T
MetaRNN	Benign	0.066	T
MetaSVM	Benign	-0.95	T
PhyloP100		0.13
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-0.49	N
REVEL	Benign	0.022
Sift	Benign	0.33	T
Sift4G	Benign	0.34	T
Polyphen		0.035	B
Vest4		0.15
MutPred		0.11		Gain of glycosylation at P94 (P = 0.0794);
MVP		0.23
MPC		0.73
ClinPred		0.17	T
GERP RS		-3.5
Varity_R		0.042
gMVP		0.095

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr17-42030334;