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GeneBe

7-155071466-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_024012.4(HTR5A):c.567C>T(p.Ser189=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00236 in 1,614,178 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0024 ( 13 hom. )

Consequence

HTR5A
NM_024012.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.49
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]
HTR5A-AS1 (HGNC:48956): (HTR5A antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-155071466-C-T is Benign according to our data. Variant chr7-155071466-C-T is described in ClinVar as [Benign]. Clinvar id is 708987.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=-2.49 with no splicing effect.
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 GnomAdExome at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTR5ANM_024012.4 linkuse as main transcriptc.567C>T p.Ser189= synonymous_variant 1/2 ENST00000287907.3
HTR5A-AS1NR_038945.1 linkuse as main transcriptn.92G>A non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTR5AENST00000287907.3 linkuse as main transcriptc.567C>T p.Ser189= synonymous_variant 1/21 NM_024012.4 P1
HTR5A-AS1ENST00000671665.1 linkuse as main transcriptn.985G>A non_coding_transcript_exon_variant 1/2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00162
AC:
246
AN:
152196
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000700
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00275
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00372
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00207
Gnomad OTH
AF:
0.00717
GnomAD3 exomes
AF:
0.00227
AC:
571
AN:
251204
Hom.:
2
AF XY:
0.00239
AC XY:
324
AN XY:
135794
show subpopulations
Gnomad AFR exome
AF:
0.000493
Gnomad AMR exome
AF:
0.00390
Gnomad ASJ exome
AF:
0.000595
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00408
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00235
Gnomad OTH exome
AF:
0.00473
GnomAD4 exome
AF:
0.00243
AC:
3555
AN:
1461864
Hom.:
13
Cov.:
35
AF XY:
0.00251
AC XY:
1826
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.00418
Gnomad4 ASJ exome
AF:
0.000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00442
Gnomad4 FIN exome
AF:
0.000356
Gnomad4 NFE exome
AF:
0.00249
Gnomad4 OTH exome
AF:
0.00268
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00162
AC:
247
AN:
152314
Hom.:
0
Cov.:
33
AF XY:
0.00141
AC XY:
105
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.000698
Gnomad4 AMR
AF:
0.00274
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00393
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00207
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00143
Hom.:
0
Bravo
AF:
0.00201
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.00284
EpiControl
AF:
0.00255

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
-0.66
Cadd
Benign
8.6
Dann
Benign
0.92

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: rs149473122; hg19: chr7-154863176; API