chr11-113910259-T-C

Position:

• chr11-113910259-T-C

Variant summary

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

The NM_006028.5(HTR3B):​c.213+804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,202 control chromosomes in the GnomAD database, including 385 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 0.060 (385 hom., cov: 31)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR3B	NM_006028.5	c.213+804T>C		intron_variant		ENST00000260191.8	NP_006019.1
HTR3B	NM_001363563.2	c.180+804T>C		intron_variant			NP_001350492.1
HTR3B	XM_024448767.2	c.-82+804T>C		intron_variant			XP_024304535.1
HTR3B	XM_047427869.1	c.180+804T>C		intron_variant			XP_047283825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR3B	ENST00000260191.8	c.213+804T>C		intron_variant		1	NM_006028.5	ENSP00000260191	P2
HTR3B	ENST00000537778.5	c.180+804T>C		intron_variant		1		ENSP00000443118	A2

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9195 AN: 152084 Hom.: 385 Cov.: 31

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0604 AC: 9194 AN: 152202 Hom.: 385 Cov.: 31 AF XY: 0.0616 AC XY: 4585 AN XY: 74422

Gnomad4 AFR AF: 0.0155

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.0358

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0830

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0755 Hom.: 247

Bravo AF: 0.0543

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.60

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: rs11606194; hg19: chr11-113780981;