rs45460698

Variant names:

• chr11-113904829-GAGA-G
• rs45460698
• NM_006028.5:c.-102_-100delAAG

Your query was ambiguous. Multiple possible variants found:

• chr11-113904829-GAGA-G
• chr11-113904829-GAGA-GAGAAGA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006028.5(HTR3B):​c.-102_-100delAAG 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 11 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 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.-102_-100delAAG		5_prime_UTR	Exon 1 of 9	NP_006019.1	O95264-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR3B	ENST00000260191.8	TSL:1 MANE Select	c.-102_-100delAAG		5_prime_UTR	Exon 1 of 9	ENSP00000260191.2	O95264-1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17811 AN: 152046 Hom.: 1055 Cov.: 30

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

African (AFR) AF: 0.113 AC: 2205 AN: 19468

American (AMR) AF: 0.0637 AC: 2537 AN: 39852

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 2500 AN: 20274

East Asian (EAS) AF: 0.153 AC: 5511 AN: 35996

South Asian (SAS) AF: 0.0999 AC: 6784 AN: 67888

European-Finnish (FIN) AF: 0.132 AC: 6792 AN: 51612

Middle Eastern (MID) AF: 0.222 AC: 950 AN: 4272

European-Non Finnish (NFE) AF: 0.123 AC: 56602 AN: 460114

Other (OTH) AF: 0.121 AC: 4380 AN: 36220

GnomAD4 genome AF: 0.117 AC: 17804 AN: 152164 Hom.: 1055 Cov.: 30 AF XY: 0.117 AC XY: 8694 AN XY: 74364

African (AFR) AF: 0.108 AC: 4502 AN: 41524

American (AMR) AF: 0.100 AC: 1536 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3466

East Asian (EAS) AF: 0.147 AC: 759 AN: 5178

South Asian (SAS) AF: 0.0905 AC: 436 AN: 4820

European-Finnish (FIN) AF: 0.134 AC: 1412 AN: 10576

Middle Eastern (MID) AF: 0.183 AC: 53 AN: 290

European-Non Finnish (NFE) AF: 0.122 AC: 8270 AN: 68000

Other (OTH) AF: 0.128 AC: 271 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.64
Mutation Taster		=300/0	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: rs45460698; hg19: chr11-113775551;