rs1672717

chr11-113942011-G-Achr11-113942011-G-Cchr11-113942011-G-T

Variant summary

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

The NM_006028.5(HTR3B):c.697-971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,136 control chromosomes in the GnomAD database, including 39,996 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 0.71 (39996 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	NM_006028.5	c.697-971G>A		intron_variant		ENST00000260191.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR3B	ENST00000260191.8	c.697-971G>A		intron_variant		1	NM_006028.5	P2
HTR3B	ENST00000537778.5	c.664-971G>A		intron_variant		1		A2
HTR3B	ENST00000543092.1	c.483-2562G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108113 AN: 152018 Hom.: 39932 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.711 AC: 108235 AN: 152136 Hom.: 39996 Cov.: 32 AF XY: 0.712 AC XY: 52920 AN XY: 74378

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.728

Alfa AF: 0.627 Hom.: 61249

Bravo AF: 0.728

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.7
Dann	Benign	0.35

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: rs1672717; hg19: chr11-113812733;