rs10061244

Variant summary

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

The NM_001040169.2(HTR4):​c.1077-27313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,134 control chromosomes in the GnomAD database, including 1,767 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 0.12 ( 1767 hom., cov: 32)

Consequence

HTR4
NM_001040169.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00500
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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HTR4NM_001040169.2 linkuse as main transcriptc.1077-27313T>C intron_variant NP_001035259.1 Q13639-2
HTR4NM_199453.3 linkuse as main transcriptc.1077-12660T>C intron_variant NP_955525.1 Q13639-5
HTR4NM_001040172.2 linkuse as main transcriptc.1077-1840T>C intron_variant NP_001035262.2 Q13639-3
LOC107986462XR_001742935.2 linkuse as main transcriptn.441+9568A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HTR4ENST00000521530.6 linkuse as main transcriptc.1077-27313T>C intron_variant 1 ENSP00000428320.1 Q13639-2
HTR4ENST00000521735.5 linkuse as main transcriptc.1077-12660T>C intron_variant 1 ENSP00000430979.1 Q13639-5
HTR4ENST00000517929.5 linkuse as main transcriptc.1077-1840T>C intron_variant 1 ENSP00000435904.1 Q13639-3
HTR4ENST00000522588.5 linkuse as main transcriptn.1077-12660T>C intron_variant 1 ENSP00000430874.1 Q13639-5

Frequencies

GnomAD3 genomes
AF:
0.122
AC:
18521
AN:
152016
Hom.:
1766
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.0525
Gnomad ASJ
AF:
0.0317
Gnomad EAS
AF:
0.167
Gnomad SAS
AF:
0.0714
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0616
Gnomad OTH
AF:
0.101
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.122
AC:
18549
AN:
152134
Hom.:
1767
Cov.:
32
AF XY:
0.122
AC XY:
9067
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.260
Gnomad4 AMR
AF:
0.0524
Gnomad4 ASJ
AF:
0.0317
Gnomad4 EAS
AF:
0.166
Gnomad4 SAS
AF:
0.0708
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.0616
Gnomad4 OTH
AF:
0.100
Alfa
AF:
0.122
Hom.:
260
Bravo
AF:
0.123
Asia WGS
AF:
0.107
AC:
372
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.1
DANN
Benign
0.56

Splicing

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: rs10061244; hg19: chr5-147858148; API