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7-155084262-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_024012.4(HTR5A):c.849C>T(p.Ala283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00352 in 1,614,106 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 40 hom., cov: 31)
Exomes 𝑓: 0.0025 ( 42 hom. )

Consequence

HTR5A
NM_024012.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.51
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-155084262-C-T is Benign according to our data. Variant chr7-155084262-C-T is described in ClinVar as [Benign]. Clinvar id is 783513.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.51 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0133 (2029/152238) while in subpopulation AFR AF= 0.0409 (1700/41524). AF 95% confidence interval is 0.0393. There are 40 homozygotes in gnomad4. There are 992 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 39 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTR5ANM_024012.4 linkuse as main transcriptc.849C>T p.Ala283= synonymous_variant 2/2 ENST00000287907.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTR5AENST00000287907.3 linkuse as main transcriptc.849C>T p.Ala283= synonymous_variant 2/21 NM_024012.4 P1
HTR5AENST00000486819.1 linkuse as main transcriptn.205C>T non_coding_transcript_exon_variant 2/21
HTR5AENST00000649716.1 linkuse as main transcriptc.*318C>T 3_prime_UTR_variant, NMD_transcript_variant 3/3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0133
AC:
2025
AN:
152120
Hom.:
39
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0410
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0120
Gnomad ASJ
AF:
0.0138
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.000955
Gnomad OTH
AF:
0.0119
GnomAD3 exomes
AF:
0.00485
AC:
1219
AN:
251358
Hom.:
17
AF XY:
0.00386
AC XY:
524
AN XY:
135860
show subpopulations
Gnomad AFR exome
AF:
0.0436
Gnomad AMR exome
AF:
0.00538
Gnomad ASJ exome
AF:
0.0156
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00108
Gnomad OTH exome
AF:
0.00652
GnomAD4 exome
AF:
0.00250
AC:
3655
AN:
1461868
Hom.:
42
Cov.:
32
AF XY:
0.00223
AC XY:
1622
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0430
Gnomad4 AMR exome
AF:
0.00617
Gnomad4 ASJ exome
AF:
0.0160
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000174
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000996
Gnomad4 OTH exome
AF:
0.00561
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0133
AC:
2029
AN:
152238
Hom.:
40
Cov.:
31
AF XY:
0.0133
AC XY:
992
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.0409
Gnomad4 AMR
AF:
0.0120
Gnomad4 ASJ
AF:
0.0138
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000956
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.00620
Hom.:
5
Bravo
AF:
0.0150
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.00196
EpiControl
AF:
0.00178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
Cadd
Benign
0.031
Dann
Benign
0.66

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: rs113935396; hg19: chr7-154875972; API