chr11-113930946-G-A

Variant names:

• chr11-113930946-G-A
• rs17116121
• NM_006028.5:c.214-438G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006028.5(HTR3B):​c.214-438G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,108 control chromosomes in the GnomAD database, including 274 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 0.053 (274 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 = 0.0794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006028.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	NM_006028.5	MANE Select	c.214-438G>A		intron	N/A	NP_006019.1
	HTR3B	NM_001363563.2		c.181-438G>A		intron	N/A	NP_001350492.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	ENST00000260191.8	TSL:1 MANE Select	c.214-438G>A		intron	N/A	ENSP00000260191.2
	HTR3B	ENST00000537778.5	TSL:1	c.181-438G>A		intron	N/A	ENSP00000443118.1

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8048 AN: 151990 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0530 AC: 8056 AN: 152108 Hom.: 274 Cov.: 32 AF XY: 0.0565 AC XY: 4201 AN XY: 74360

African (AFR) AF: 0.0817 AC: 3389 AN: 41498

American (AMR) AF: 0.0714 AC: 1091 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1064 AN: 10536

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2100 AN: 68004

Other (OTH) AF: 0.0460 AC: 97 AN: 2110

Alfa AF: 0.0344 Hom.: 52

Bravo AF: 0.0494

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.60
PhyloP100		0.12
PromoterAI		0.0078	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs17116121; hg19: chr11-113801668;