rs17614942

chr11-113945655-C-A

Variant summary

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

The NM_006028.5(HTR3B):c.1091-247C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 152,282 control chromosomes in the GnomAD database, including 383 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 0.065 (383 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

HTR3B (HGNC:5298): (5-hydroxytryptamine receptor 3B) The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit B 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. It is not functional as a homomeric complex, but a pentaheteromeric complex with subunit A (HTR3A) displays the full functional features of this receptor. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	NM_006028.5	c.1091-247C>A		intron_variant		ENST00000260191.8
HTR3B	NM_001363563.2	c.1058-247C>A		intron_variant
HTR3B	XM_017018552.3	c.884-247C>A		intron_variant
HTR3B	XM_024448767.2	c.797-247C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR3B	ENST00000260191.8	c.1091-247C>A		intron_variant		1	NM_006028.5	P2
HTR3B	ENST00000537778.5	c.1058-247C>A		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9811 AN: 152164 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.0297

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0737

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0645 AC: 9823 AN: 152282 Hom.: 383 Cov.: 32 AF XY: 0.0625 AC XY: 4652 AN XY: 74468

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0297

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0658 Hom.: 347

Bravo AF: 0.0689

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.2
Dann	Benign	0.73

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: rs17614942; hg19: chr11-113816377;