rs6807670

chr3-184060510-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130770.3(HTR3C):c.*158G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 927,970 control chromosomes in the GnomAD database, including 180,257 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (28462 hom., cov: 31)
  • Exomes 𝑓: 0.62 (151795 hom.)
• Consequence: HTR3C NM_130770.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846

Genes affected

HTR3C (HGNC:24003): (5-hydroxytryptamine receptor 3C) The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit C of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor causes fast, depolarizing responses in neurons after activation. Genes encoding subunits C, D and E form a cluster on chromosome 3. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3C	NM_130770.3	c.*158G>A		3_prime_UTR_variant	9/9	ENST00000318351.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR3C	ENST00000318351.2	c.*158G>A		3_prime_UTR_variant	9/9	1	NM_130770.3	P1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92425 AN: 151758 Hom.: 28456 Cov.: 31

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.622

GnomAD4 exome AF: 0.623 AC: 483296 AN: 776094 Hom.: 151795 Cov.: 10 AF XY: 0.620 AC XY: 246842 AN XY: 397950

Gnomad4 AFR exome AF: 0.527

Gnomad4 AMR exome AF: 0.724

Gnomad4 ASJ exome AF: 0.714

Gnomad4 EAS exome AF: 0.756

Gnomad4 SAS exome AF: 0.561

Gnomad4 FIN exome AF: 0.673

Gnomad4 NFE exome AF: 0.611

Gnomad4 OTH exome AF: 0.636

GnomAD4 genome AF: 0.609 AC: 92455 AN: 151876 Hom.: 28462 Cov.: 31 AF XY: 0.613 AC XY: 45473 AN XY: 74198

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.625

Alfa AF: 0.627 Hom.: 46030

Bravo AF: 0.610

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.56

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: rs6807670; hg19: chr3-183778298; COSMIC: COSV59174610;