rs2067470

Variant names:

• chr3-11260383-T-C
• rs2067470
• NM_001098212.2:c.1346T>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001098212.2(HRH1):​c.1346T>C​(p.Leu449Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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: 0.0000014 (0 hom.)
• Consequence: HRH1 NM_001098212.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.06

Genes affected

HRH1 (HGNC:5182): (histamine receptor H1) Histamine is a ubiquitous messenger molecule released from mast cells, enterochromaffin-like cells, and neurons. Its various actions are mediated by histamine receptors H1, H2, H3 and H4. The protein encoded by this gene is an integral membrane protein and belongs to the G protein-coupled receptor superfamily. It mediates the contraction of smooth muscles, the increase in capillary permeability due to contraction of terminal venules, the release of catecholamine from adrenal medulla, and neurotransmission in the central nervous system. It has been associated with multiple processes, including memory and learning, circadian rhythm, and thermoregulation. It is also known to contribute to the pathophysiology of allergic diseases such as atopic dermatitis, asthma, anaphylaxis and allergic rhinitis. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3375491).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HRH1	NM_001098212.2	c.1346T>C	p.Leu449Ser	missense_variant	Exon 2 of 2	ENST00000431010.3	NP_001091682.1
HRH1	NM_000861.3	c.1346T>C	p.Leu449Ser	missense_variant	Exon 3 of 3		NP_000852.1
HRH1	NM_001098211.2	c.1346T>C	p.Leu449Ser	missense_variant	Exon 2 of 2		NP_001091681.1
HRH1	NM_001098213.2	c.1346T>C	p.Leu449Ser	missense_variant	Exon 2 of 2		NP_001091683.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HRH1	ENST00000431010.3	c.1346T>C	p.Leu449Ser	missense_variant	Exon 2 of 2	1	NM_001098212.2	ENSP00000397028.2
HRH1	ENST00000397056.1	c.1346T>C	p.Leu449Ser	missense_variant	Exon 3 of 3	1		ENSP00000380247.1
HRH1	ENST00000438284.2	c.1346T>C	p.Leu449Ser	missense_variant	Exon 2 of 2	2		ENSP00000406705.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461888 Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2 AN XY: 727244

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: 8.99e-7

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	0.28
BayesDel_addAF	Benign	-0.046	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.33	T;T;T
Eigen	Benign	0.10
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.75	.;.;T
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.34	T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.7	L;L;L
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-4.3	D;D;D
REVEL	Benign	0.14
Sift	Uncertain	0.0040	D;D;D
Sift4G	Uncertain	0.0080	D;D;D
Polyphen		0.38	B;B;B
Vest4		0.46
MutPred		0.54		Gain of glycosylation at L449 (P = 0.02);Gain of glycosylation at L449 (P = 0.02);Gain of glycosylation at L449 (P = 0.02);
MVP		0.77
MPC		0.77
ClinPred		0.98	D
GERP RS		4.9
Varity_R		0.30
gMVP		0.83

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: rs2067470; hg19: chr3-11302069;