11-113942011-G-A

Variant names:

• chr11-113942011-G-A
• rs1672717
• NM_006028.5:c.697-971G>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.697-971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,136 control chromosomes in the GnomAD database, including 39,996 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 0.71 (39996 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 24 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	NM_006028.5	MANE Select	c.697-971G>A		intron	N/A	NP_006019.1
	HTR3B	NM_001363563.2		c.664-971G>A		intron	N/A	NP_001350492.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	ENST00000260191.8	TSL:1 MANE Select	c.697-971G>A		intron	N/A	ENSP00000260191.2
	HTR3B	ENST00000537778.5	TSL:1	c.664-971G>A		intron	N/A	ENSP00000443118.1
	HTR3B	ENST00000543092.1	TSL:3	c.481-2562G>A		intron	N/A	ENSP00000440894.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108113 AN: 152018 Hom.: 39932 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.711 AC: 108235 AN: 152136 Hom.: 39996 Cov.: 32 AF XY: 0.712 AC XY: 52920 AN XY: 74378

African (AFR) AF: 0.917 AC: 38103 AN: 41542

American (AMR) AF: 0.745 AC: 11378 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2335 AN: 3466

East Asian (EAS) AF: 0.674 AC: 3481 AN: 5162

South Asian (SAS) AF: 0.673 AC: 3245 AN: 4822

European-Finnish (FIN) AF: 0.595 AC: 6293 AN: 10568

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41091 AN: 67986

Other (OTH) AF: 0.728 AC: 1540 AN: 2114

Alfa AF: 0.638 Hom.: 134672

Bravo AF: 0.728

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.35
PhyloP100		0.56
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: rs1672717; hg19: chr11-113812733;