Variant rs45460698 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006028.5(HTR3B):c.-102_-100del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 887,860 control chromosomes in the GnomAD database, including 6,629 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1055 hom., cov: 30)

Exomes 𝑓: 0.12 ( 5574 hom. )

Consequence

HTR3B
NM_006028.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.639

Variant links:

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]

HTR3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	NM_006028.5 linkuse as main transcript	c.-102_-100del		5_prime_UTR_variant	1/9	ENST00000260191.8
HTR3B	XM_024448767.2 linkuse as main transcript	c.-242-4463_-242-4461del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR3B	ENST00000260191.8 linkuse as main transcript	c.-102_-100del		5_prime_UTR_variant	1/9	1	NM_006028.5	P2	O95264-1

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17811

AN:

152046

Hom.:

1055

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.0920

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.186

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.120

AC:

88261

AN:

735696

Hom.:

5574

AF XY:

0.120

AC XY:

46946

AN XY:

391042

show subpopulations

Gnomad4 AFR exome

AF:

0.113

Gnomad4 AMR exome

AF:

0.0637

Gnomad4 ASJ exome

AF:

0.123

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.0999

Gnomad4 FIN exome

AF:

0.132

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.121

GnomAD4 genome

AF:

0.117

AC:

17804

AN:

152164

Hom.:

1055

Cov.:

AF XY:

0.117

AC XY:

8694

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.100

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.0905

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.112

Hom.:

124

Bravo

AF:

0.115

Asia WGS

AF:

0.110

AC:

382

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over