NM_006028.5:c.696+511C>T

Variant names:

• chr11-113933604-C-T
• rs17116145
• NM_006028.5:c.696+511C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006028.5(HTR3B):​c.696+511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 152,116 control chromosomes in the GnomAD database, including 275 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 0.053 (275 hom., cov: 32)
• Consequence: HTR3B NM_006028.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR3B	NM_006028.5	c.696+511C>T		intron_variant	Intron 6 of 8	ENST00000260191.8	NP_006019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR3B	ENST00000260191.8	c.696+511C>T		intron_variant	Intron 6 of 8	1	NM_006028.5	ENSP00000260191.2
HTR3B	ENST00000537778.5	c.663+511C>T		intron_variant	Intron 5 of 7	1		ENSP00000443118.1
HTR3B	ENST00000543092.1	c.480+511C>T		intron_variant	Intron 4 of 4	3		ENSP00000440894.1

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8043 AN: 151998 Hom.: 274 Cov.: 32

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0529 AC: 8051 AN: 152116 Hom.: 275 Cov.: 32 AF XY: 0.0565 AC XY: 4199 AN XY: 74358

African (AFR) AF: 0.0814 AC: 3376 AN: 41486

American (AMR) AF: 0.0714 AC: 1090 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 63 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4816

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10566

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2103 AN: 68010

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0453 Hom.: 42

Bravo AF: 0.0493

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.3
DANN	Benign	0.83
PhyloP100		0.33
Mutation Taster		=100/0	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: rs17116145; hg19: chr11-113804326;