rs2454727

chr12-122702333-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_177551.4(HCAR2):c.951G>A(p.Met317Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.23 (3 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCAR2 NM_177551.4 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -4.12

Genes affected

HCAR2 (HGNC:24827): (hydroxycarboxylic acid receptor 2) Predicted to enable nicotinic acid receptor activity. Involved in neutrophil apoptotic process and positive regulation of neutrophil apoptotic process. Located in cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0018282831).
• BP6: Variant 12-122702333-C-T is Benign according to our data. Variant chr12-122702333-C-T is described in ClinVar as [Benign]. Clinvar id is 770415.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCAR2	NM_177551.4	c.951G>A	p.Met317Ile	missense_variant	1/1	ENST00000328880.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCAR2	ENST00000328880.6	c.951G>A	p.Met317Ile	missense_variant	1/1		NM_177551.4	P1
	ENST00000543611.1	n.401+1003C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 33186 AN: 145294 Hom.: 3 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.239

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.121 AC: 140790 AN: 1166210 Hom.: 1 Cov.: 42 AF XY: 0.124 AC XY: 72600 AN XY: 583724

Gnomad4 AFR exome AF: 0.0545

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.215

Gnomad4 EAS exome AF: 0.0201

Gnomad4 SAS exome AF: 0.130

Gnomad4 FIN exome AF: 0.209

Gnomad4 NFE exome AF: 0.119

Gnomad4 OTH exome AF: 0.146

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.228 AC: 33180 AN: 145410 Hom.: 3 Cov.: 32 AF XY: 0.224 AC XY: 15850 AN XY: 70798

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.235

Alfa AF: 0.240 Hom.: 4

ExAC AF: 0.184 AC: 22340

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 13, 2018	This variant is associated with the following publications: (PMID: 25363768) -
Benign, criteria provided, single submitter	clinical testing	Invitae	Mar 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	-0.77	T
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.0030
Dann	Benign	0.69
DEOGEN2	Benign	0.064	T
Eigen	Benign	-2.1
Eigen_PC	Benign	-2.2
FATHMM_MKL	Benign	0.018	N
LIST_S2	Benign	0.20	T
MetaRNN	Benign	0.0018	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
MutationTaster	Benign	1.0	P;P
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.59	N
REVEL	Benign	0.035
Sift	Benign	0.45	T
Sift4G	Benign	0.42	T
Polyphen		0.0	B
Vest4		0.017
MutPred		0.11		Gain of methylation at K316 (P = 0.024);
MPC		0.80
ClinPred		0.0070	T
GERP RS		-11
Varity_R		0.047
gMVP		0.14

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: rs2454727; hg19: chr12-123186880; COSMIC: COSV61024117;