rs7103572

Positions:

• chr11-113919377-C-T

Variant summary

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

The NM_006028.5(HTR3B):​c.213+9922C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,968 control chromosomes in the GnomAD database, including 5,286 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 0.26 (5286 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

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 (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR3B	NM_006028.5	c.213+9922C>T		intron_variant		ENST00000260191.8	NP_006019.1
HTR3B	NM_001363563.2	c.180+9922C>T		intron_variant			NP_001350492.1
HTR3B	XM_024448767.2	c.-82+9922C>T		intron_variant			XP_024304535.1
HTR3B	XM_047427869.1	c.180+9922C>T		intron_variant			XP_047283825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR3B	ENST00000260191.8	c.213+9922C>T		intron_variant		1	NM_006028.5	ENSP00000260191.2
HTR3B	ENST00000537778.5	c.180+9922C>T		intron_variant		1		ENSP00000443118.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39604 AN: 151852 Hom.: 5285 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.261 AC: 39627 AN: 151968 Hom.: 5286 Cov.: 32 AF XY: 0.257 AC XY: 19120 AN XY: 74286

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.265

Alfa AF: 0.276 Hom.: 1295

Bravo AF: 0.262

Asia WGS AF: 0.263 AC: 915 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.16

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: rs7103572; hg19: chr11-113790099;