rs33954285

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_019859.4(HTR7):​c.1343C>T​(p.Pro448Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P448Q) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )

Consequence

HTR7
NM_019859.4 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12
Variant links:
Genes affected
HTR7 (HGNC:5302): (5-hydroxytryptamine receptor 7) The neurotransmitter, serotonin, is thought to play a role in various cognitive and behavioral functions. The serotonin receptor encoded by this gene belongs to the superfamily of G protein-coupled receptors and the gene is a candidate locus for involvement in autistic disorder and other neuropsychiatric disorders. Three splice variants have been identified which encode proteins that differ in the length of their carboxy terminal ends. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04305619).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HTR7NM_019859.4 linkc.1343C>T p.Pro448Leu missense_variant Exon 3 of 4 ENST00000336152.8 NP_062873.1 P34969-1
HTR7XM_024447973.2 linkc.749C>T p.Pro250Leu missense_variant Exon 3 of 4 XP_024303741.1
HTR7NM_000872.5 linkc.1296-1115C>T intron_variant Intron 2 of 2 NP_000863.1 P34969-2
HTR7NM_019860.4 linkc.*2-1115C>T intron_variant Intron 2 of 2 NP_062874.1 P34969-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HTR7ENST00000336152.8 linkc.1343C>T p.Pro448Leu missense_variant Exon 3 of 4 1 NM_019859.4 ENSP00000337949.3 P34969-1
HTR7ENST00000277874.10 linkc.1296-1115C>T intron_variant Intron 2 of 2 1 ENSP00000277874.6 P34969-2
HTR7ENST00000371719.2 linkc.*2-1115C>T intron_variant Intron 2 of 2 1 ENSP00000360784.2 P34969-3

Frequencies

GnomAD3 genomes
AF:
0.0000329
AC:
5
AN:
152086
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000107
AC:
27
AN:
251380
Hom.:
1
AF XY:
0.0000957
AC XY:
13
AN XY:
135856
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.000463
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000616
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.0000547
AC:
80
AN:
1461706
Hom.:
0
Cov.:
31
AF XY:
0.0000550
AC XY:
40
AN XY:
727150
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000403
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000432
Gnomad4 OTH exome
AF:
0.000166
GnomAD4 genome
AF:
0.0000329
AC:
5
AN:
152086
Hom.:
0
Cov.:
32
AF XY:
0.0000404
AC XY:
3
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.0000483
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000215
Hom.:
6
Bravo
AF:
0.0000831
ExAC
AF:
0.0000494
AC:
6
EpiCase
AF:
0.000109
EpiControl
AF:
0.000178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.50
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
0.10
DANN
Benign
0.89
DEOGEN2
Benign
0.14
T
Eigen
Benign
-2.2
Eigen_PC
Benign
-2.2
FATHMM_MKL
Benign
0.0044
N
LIST_S2
Benign
0.32
T
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.043
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-0.10
N
REVEL
Benign
0.034
Sift
Benign
0.057
T
Sift4G
Pathogenic
0.0
D
Polyphen
0.0010
B
Vest4
0.11
MutPred
0.29
Loss of catalytic residue at P447 (P = 0.016);
MVP
0.61
MPC
0.42
ClinPred
0.035
T
GERP RS
-3.8
Varity_R
0.026
gMVP
0.15

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: rs33954285; hg19: chr10-92503400; COSMIC: COSV53292379; API