chr1-31626924-A-C

Variant names:

• chr1-31626924-A-C
• rs2271933
• NM_001525.3:c.1222A>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001525.3(HCRTR1):​c.1222A>C​(p.Ile408Leu) 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. 16/22 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)
• Consequence: HCRTR1 NM_001525.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 0 publications found

Genes affected

HCRTR1 (HGNC:4848): (hypocretin receptor 1) The protein encoded by this gene is a G-protein coupled receptor involved in the regulation of feeding behavior. The encoded protein selectively binds the hypothalamic neuropeptide orexin A. A related gene (HCRTR2) encodes a G-protein coupled receptor that binds orexin A and orexin B. [provided by RefSeq, Jan 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.083266795).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCRTR1	NM_001525.3	c.1222A>C	p.Ile408Leu	missense_variant	Exon 9 of 9	ENST00000403528.7	NP_001516.2
HCRTR1	XM_024446605.2	c.1222A>C	p.Ile408Leu	missense_variant	Exon 10 of 11		XP_024302373.1
HCRTR1	XM_017001107.2	c.1087+1806A>C		intron_variant	Intron 6 of 6		XP_016856596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCRTR1	ENST00000403528.7	c.1222A>C	p.Ile408Leu	missense_variant	Exon 9 of 9	5	NM_001525.3	ENSP00000384387.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 55

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	16
DANN	Uncertain	0.98
DEOGEN2	Benign	0.040	T;T
Eigen	Benign	-0.72
Eigen_PC	Benign	-0.53
FATHMM_MKL	Benign	0.62	D
LIST_S2	Benign	0.14	T;.
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.083	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.20	N;N
PhyloP100		1.8
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.14	N;N
REVEL	Benign	0.093
Sift	Benign	0.16	T;T
Sift4G	Benign	0.59	T;T
Polyphen		0.083	B;B
Vest4		0.11
MutPred		0.14		Loss of MoRF binding (P = 0.1285);Loss of MoRF binding (P = 0.1285);
MVP		0.47
MPC		0.33
ClinPred		0.16	T
GERP RS		3.8
Varity_R		0.069
gMVP		0.079
Mutation Taster		=99/1	polymorphism

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

Other links and lift over

dbSNP: rs2271933; hg19: chr1-32092525;