11-113907040-T-G

Variant names:

• chr11-113907040-T-G
• rs10502180
• NM_006028.5:c.52+2055T>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.52+2055T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,298 control chromosomes in the GnomAD database, including 460 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 0.038 (460 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR3B	NM_006028.5	c.52+2055T>G		intron_variant	Intron 1 of 8	ENST00000260191.8	NP_006019.1
HTR3B	XM_024448767.2	c.-242-2255T>G		intron_variant	Intron 1 of 8		XP_024304535.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR3B	ENST00000260191.8	c.52+2055T>G		intron_variant	Intron 1 of 8	1	NM_006028.5	ENSP00000260191.2

Frequencies

GnomAD3 genomes AF: 0.0383 AC: 5823 AN: 152180 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00822

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0385 AC: 5856 AN: 152298 Hom.: 460 Cov.: 32 AF XY: 0.0417 AC XY: 3108 AN XY: 74474

African (AFR) AF: 0.0307 AC: 1275 AN: 41564

American (AMR) AF: 0.125 AC: 1909 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1568 AN: 5172

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4828

European-Finnish (FIN) AF: 0.00603 AC: 64 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00823 AC: 560 AN: 68034

Other (OTH) AF: 0.0488 AC: 103 AN: 2112

Alfa AF: 0.0206 Hom.: 181

Bravo AF: 0.0507

Asia WGS AF: 0.189 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.60
PhyloP100		0.95
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: rs10502180; hg19: chr11-113777762;