Variant rs6320 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_024012.4(HTR5A):c.12T>A(p.Pro4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 1,600,956 control chromosomes in the GnomAD database, including 65,314 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 ( 5281 hom., cov: 32)

Exomes 𝑓: 0.28 ( 60033 hom. )

Consequence

HTR5A
NM_024012.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.736

Variant links:

Genes affected

HTR5A (HGNC:5300): (5-hydroxytryptamine receptor 5A) The neurotransmitter serotonin (5-hydroxytryptamine, 5-HT) has been implicated in a wide range of psychiatric conditions and also has vasoconstrictive and vasodilatory effects. The gene described in this record is a member of 5-hydroxytryptamine (serotonin) receptor family and encodes a multi-pass membrane protein that functions as a receptor for 5-hydroxytryptamine and couples to G-proteins. This protein has been shown to function in part through the regulation of intracellular Ca2+ mobilization. [provided by RefSeq, Jul 2008]

HTR5A links:

HTR5A-AS1 (HGNC:48956): (HTR5A antisense RNA 1)

HTR5A-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=-0.736 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR5A	NM_024012.4 linkuse as main transcript	c.12T>A	p.Pro4=	synonymous_variant	1/2	ENST00000287907.3
HTR5A-AS1	NR_038945.1 linkuse as main transcript	n.524+123A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR5A	ENST00000287907.3 linkuse as main transcript	c.12T>A	p.Pro4=	synonymous_variant	1/2	1	NM_024012.4	P1
HTR5A-AS1	ENST00000671665.1 linkuse as main transcript	n.1417+123A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39345

AN:

151972

Hom.:

5281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.286

Gnomad OTH

AF:

0.269

GnomAD3 exomes

AF:

0.262

AC:

63551

AN:

242472

Hom.:

8692

AF XY:

0.262

AC XY:

34548

AN XY:

131694

show subpopulations

Gnomad AFR exome

AF:

0.213

Gnomad AMR exome

AF:

0.202

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.385

Gnomad SAS exome

AF:

0.235

Gnomad FIN exome

AF:

0.268

Gnomad NFE exome

AF:

0.277

Gnomad OTH exome

AF:

0.273

GnomAD4 exome

AF:

0.285

AC:

412353

AN:

1448866

Hom.:

60033

Cov.:

AF XY:

0.283

AC XY:

204262

AN XY:

720934

show subpopulations

Gnomad4 AFR exome

AF:

0.216

Gnomad4 AMR exome

AF:

0.207

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.390

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.263

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.259

AC:

39366

AN:

152090

Hom.:

5281

Cov.:

AF XY:

0.257

AC XY:

19137

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.225

Gnomad4 ASJ

AF:

0.227

Gnomad4 EAS

AF:

0.368

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.286

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.198

Hom.:

640

Bravo

AF:

0.257

Asia WGS

AF:

0.286

AC:

993

AN:

3478

EpiCase

AF:

0.275

EpiControl

AF:

0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.7

DANN

Benign

0.84

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