7-155083756-G-A

Variant summary

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

The NM_024012.4(HTR5A):​c.742-399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 152,260 control chromosomes in the GnomAD database, including 201 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 0.029 ( 201 hom., cov: 32)

Consequence

HTR5A
NM_024012.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.649
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]

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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 (AFR) allele frequency at 95% confidence interval = 0.099 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTR5ANM_024012.4 linkuse as main transcriptc.742-399G>A intron_variant ENST00000287907.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTR5AENST00000287907.3 linkuse as main transcriptc.742-399G>A intron_variant 1 NM_024012.4 P1
HTR5AENST00000486819.1 linkuse as main transcriptn.98-399G>A intron_variant, non_coding_transcript_variant 1
HTR5AENST00000649716.1 linkuse as main transcriptc.*211-399G>A intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0294
AC:
4468
AN:
152142
Hom.:
201
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0112
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000470
Gnomad OTH
AF:
0.0234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0294
AC:
4475
AN:
152260
Hom.:
201
Cov.:
32
AF XY:
0.0283
AC XY:
2108
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.0111
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000470
Gnomad4 OTH
AF:
0.0232
Alfa
AF:
0.0233
Hom.:
15
Bravo
AF:
0.0335
Asia WGS
AF:
0.00375
AC:
13
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
0.82
DANN
Benign
0.72

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: rs6947679; hg19: chr7-154875466; API