rs1972644

Variant summary

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

The NM_000870.7(HTR4):​c.-47-2924G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,848 control chromosomes in the GnomAD database, including 13,814 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 0.42 ( 13814 hom., cov: 31)

Consequence

HTR4
NM_000870.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.446
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTR4NM_000870.7 linkuse as main transcriptc.-47-2924G>A intron_variant ENST00000377888.8
HTR4NR_104445.2 linkuse as main transcriptn.467-2924G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTR4ENST00000377888.8 linkuse as main transcriptc.-47-2924G>A intron_variant 1 NM_000870.7 Q13639-1

Frequencies

GnomAD3 genomes
AF:
0.424
AC:
64259
AN:
151730
Hom.:
13806
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.453
Gnomad AMI
AF:
0.559
Gnomad AMR
AF:
0.389
Gnomad ASJ
AF:
0.412
Gnomad EAS
AF:
0.536
Gnomad SAS
AF:
0.428
Gnomad FIN
AF:
0.378
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.410
Gnomad OTH
AF:
0.432
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.423
AC:
64290
AN:
151848
Hom.:
13814
Cov.:
31
AF XY:
0.423
AC XY:
31421
AN XY:
74210
show subpopulations
Gnomad4 AFR
AF:
0.452
Gnomad4 AMR
AF:
0.389
Gnomad4 ASJ
AF:
0.412
Gnomad4 EAS
AF:
0.536
Gnomad4 SAS
AF:
0.428
Gnomad4 FIN
AF:
0.378
Gnomad4 NFE
AF:
0.410
Gnomad4 OTH
AF:
0.433
Alfa
AF:
0.414
Hom.:
6300
Bravo
AF:
0.424
Asia WGS
AF:
0.490
AC:
1703
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
0.99
DANN
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1972644; hg19: chr5-148019548; API