11-113918658-A-G

Variant names:

• chr11-113918658-A-G
• rs4938058
• NM_006028.5:c.213+9203A>G

Variant summary

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

The NM_006028.5(HTR3B):​c.213+9203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 140,994 control chromosomes in the GnomAD database, including 4,888 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 0.26 (4888 hom., cov: 26)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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.213+9203A>G		intron	N/A	NP_006019.1
	HTR3B	NM_001363563.2		c.180+9203A>G		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.213+9203A>G		intron	N/A	ENSP00000260191.2
	HTR3B	ENST00000537778.5	TSL:1	c.180+9203A>G		intron	N/A	ENSP00000443118.1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 36677 AN: 140932 Hom.: 4888 Cov.: 26

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.260 AC: 36680 AN: 140994 Hom.: 4888 Cov.: 26 AF XY: 0.255 AC XY: 17323 AN XY: 67960

African (AFR) AF: 0.219 AC: 8199 AN: 37502

American (AMR) AF: 0.281 AC: 3888 AN: 13820

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 962 AN: 3380

East Asian (EAS) AF: 0.164 AC: 789 AN: 4822

South Asian (SAS) AF: 0.341 AC: 1516 AN: 4452

European-Finnish (FIN) AF: 0.179 AC: 1480 AN: 8284

Middle Eastern (MID) AF: 0.344 AC: 95 AN: 276

European-Non Finnish (NFE) AF: 0.289 AC: 18964 AN: 65606

Other (OTH) AF: 0.266 AC: 522 AN: 1964

Alfa AF: 0.0632 Hom.: 63

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.56
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4938058; hg19: chr11-113789380;