Variant rs6298 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000863.3(HTR1B):c.129C>T(p.Ser43=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,613,886 control chromosomes in the GnomAD database, including 64,085 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 0.27 ( 6051 hom., cov: 32)

Exomes 𝑓: 0.28 ( 58034 hom. )

Consequence

HTR1B
NM_000863.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.588

Variant links:

Genes affected

HTR1B (HGNC:5287): (5-hydroxytryptamine receptor 1B) The protein encoded by this intronless gene is a G-protein coupled receptor for serotonin (5-hydroxytryptamine). Ligand binding activates second messengers that inhibit the activity of adenylate cyclase and manage the release of serotonin, dopamine, and acetylcholine in the brain. The encoded protein may be involved in several neuropsychiatric disorders and therefore is often a target of antidepressant and other psychotherapeutic drugs. [provided by RefSeq, Nov 2015]

HTR1B links:

LOC105377864 (HGNC:):

LOC105377864 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP7

Synonymous conserved (PhyloP=0.588 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
HTR1B	NM_000863.3 linkuse as main transcript	c.129C>T	p.Ser43=	synonymous_variant	1/1	ENST00000369947.5
LOC105377864	XM_047419660.1 linkuse as main transcript	c.-3742-11251G>A		intron_variant
LOC105377864	XM_047419659.1 linkuse as main transcript	c.-11184G>A		5_prime_UTR_variant	2/6
LOC105377864	XM_047419661.1 linkuse as main transcript	c.-3917+157G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR1B	ENST00000369947.5 linkuse as main transcript	c.129C>T	p.Ser43=	synonymous_variant	1/1		NM_000863.3	P1

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41737

AN:

152016

Hom.:

6055

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.496

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.273

GnomAD3 exomes

AF:

0.312

AC:

78496

AN:

251480

Hom.:

13254

AF XY:

0.310

AC XY:

42097

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.237

Gnomad AMR exome

AF:

0.431

Gnomad ASJ exome

AF:

0.249

Gnomad EAS exome

AF:

0.500

Gnomad SAS exome

AF:

0.351

Gnomad FIN exome

AF:

0.245

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.299

GnomAD4 exome

AF:

0.277

AC:

404461

AN:

1461752

Hom.:

58034

Cov.:

AF XY:

0.278

AC XY:

202181

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.230

Gnomad4 AMR exome

AF:

0.426

Gnomad4 ASJ exome

AF:

0.249

Gnomad4 EAS exome

AF:

0.476

Gnomad4 SAS exome

AF:

0.354

Gnomad4 FIN exome

AF:

0.252

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.283

GnomAD4 genome

AF:

0.274

AC:

41747

AN:

152134

Hom.:

6051

Cov.:

AF XY:

0.279

AC XY:

20727

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.496

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.259

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.262

Hom.:

10794

Bravo

AF:

0.283

Asia WGS

AF:

0.395

AC:

1369

AN:

3478

EpiCase

AF:

0.263

EpiControl

AF:

0.256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

8.5

DANN

Benign

0.73

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