dbSNP rs1730208: HTR5A:c.742-85G>A (chr7-155084070-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024012.4(HTR5A):c.742-85G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,107,978 control chromosomes in the GnomAD database, including 43,600 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 0.22 ( 4654 hom., cov: 31)

Exomes 𝑓: 0.28 ( 38946 hom. )

Consequence

HTR5A
NM_024012.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

3 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A	NM_024012.4 link	c.742-85G>A		intron_variant	Intron 1 of 1	ENST00000287907.3	NP_076917.1	P47898A4D2N2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HTR5A	ENST00000287907.3 link	c.742-85G>A	intron_variant	Intron 1 of 1	1	NM_024012.4	ENSP00000287907.2	P47898
HTR5A	ENST00000486819.1 link	n.98-85G>A	intron_variant	Intron 1 of 1	1
HTR5A	ENST00000649716.1 link	n.*211-85G>A	intron_variant	Intron 2 of 2			ENSP00000497222.1	A0A3B3ISH0

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33702

AN:

151818

Hom.:

4645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0541

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.241

GnomAD4 exome

AF:

0.278

AC:

265878

AN:

956042

Hom.:

38946

AF XY:

0.280

AC XY:

133586

AN XY:

477522

show subpopulations

African (AFR)

AF:

0.0450

AC:

1006

AN:

22370

American (AMR)

AF:

0.209

AC:

4589

AN:

22004

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

4357

AN:

16944

East Asian (EAS)

AF:

0.173

AC:

5993

AN:

34674

South Asian (SAS)

AF:

0.304

AC:

17548

AN:

57808

European-Finnish (FIN)

AF:

0.380

AC:

12338

AN:

32484

Middle Eastern (MID)

AF:

0.263

AC:

1142

AN:

4346

European-Non Finnish (NFE)

AF:

0.286

AC:

206960

AN:

722416

Other (OTH)

AF:

0.278

AC:

11945

AN:

42996

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9720

19440

29159

38879

48599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.222

AC:

33716

AN:

151936

Hom.:

4654

Cov.:

AF XY:

0.225

AC XY:

16729

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.0539

AC:

2237

AN:

41486

American (AMR)

AF:

0.219

AC:

3344

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

878

AN:

3468

East Asian (EAS)

AF:

0.217

AC:

1121

AN:

5176

South Asian (SAS)

AF:

0.297

AC:

1424

AN:

4796

European-Finnish (FIN)

AF:

0.370

AC:

3898

AN:

10538

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19891

AN:

67896

Other (OTH)

AF:

0.247

AC:

522

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1256

2512

3767

5023

6279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.252

Hom.:

988

Bravo

AF:

0.202

Asia WGS

AF:

0.299

AC:

1037

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.30

(source)

DANN

Benign

0.61

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1730208

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over