rs2068190

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000870.7(HTR4):​c.26+9539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,034 control chromosomes in the GnomAD database, including 18,233 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 0.48 ( 18233 hom., cov: 33)

Consequence

HTR4
NM_000870.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470
Variant links:
Genes affected
HTR4 (HGNC:5299): (5-hydroxytryptamine receptor 4) This gene is a member of the family of serotonin receptors, which are G protein coupled receptors that stimulate cAMP production in response to serotonin (5-hydroxytryptamine). The gene product is a glycosylated transmembrane protein that functions in both the peripheral and central nervous system to modulate the release of various neurotransmitters. Multiple transcript variants encoding proteins with distinct C-terminal sequences have been described. [provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HTR4NM_000870.7 linkuse as main transcriptc.26+9539C>T intron_variant ENST00000377888.8 NP_000861.1 Q13639-1A0A2D3FAF9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HTR4ENST00000377888.8 linkuse as main transcriptc.26+9539C>T intron_variant 1 NM_000870.7 ENSP00000367120.4 Q13639-1

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
73374
AN:
151916
Hom.:
18211
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.574
Gnomad AMI
AF:
0.500
Gnomad AMR
AF:
0.424
Gnomad ASJ
AF:
0.450
Gnomad EAS
AF:
0.678
Gnomad SAS
AF:
0.553
Gnomad FIN
AF:
0.405
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.435
Gnomad OTH
AF:
0.481
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73444
AN:
152034
Hom.:
18233
Cov.:
33
AF XY:
0.482
AC XY:
35836
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.574
Gnomad4 AMR
AF:
0.423
Gnomad4 ASJ
AF:
0.450
Gnomad4 EAS
AF:
0.677
Gnomad4 SAS
AF:
0.553
Gnomad4 FIN
AF:
0.405
Gnomad4 NFE
AF:
0.435
Gnomad4 OTH
AF:
0.481
Alfa
AF:
0.445
Hom.:
31357
Bravo
AF:
0.487
Asia WGS
AF:
0.632
AC:
2194
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
6.4
DANN
Benign
0.63

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.

Other links and lift over

dbSNP: rs2068190; hg19: chr5-148007013; API