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GeneBe

rs6313

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000621.5(HTR2A):c.102C>T(p.Ser34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151936 control chromosomes in the gnomAD Genomes database, including 12506 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.40 ( 12506 hom., cov: 32)
Exomes 𝑓: 0.41 ( 21805 hom. )

Consequence

HTR2A
NM_000621.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.35

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 13-46895805-G-A is Benign according to our data. Variant chr13-46895805-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 511089.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.35 with no splicing effect.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HTR2ANM_000621.5 linkuse as main transcriptc.102C>T p.Ser34= synonymous_variant 2/4 ENST00000542664.4
HTR2ANM_001378924.1 linkuse as main transcriptc.102C>T p.Ser34= synonymous_variant 2/4
HTR2ANM_001165947.5 linkuse as main transcriptc.-78+869C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HTR2AENST00000542664.4 linkuse as main transcriptc.102C>T p.Ser34= synonymous_variant 2/41 NM_000621.5 P1P28223-1
HTR2AENST00000543956.5 linkuse as main transcriptc.-78+869C>T intron_variant 1
HTR2AENST00000612998.1 linkuse as main transcriptc.9C>T p.Ser3= synonymous_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.402
AC:
61037
AN:
151936
Hom.:
12506
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.378
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.390
Gnomad ASJ
AF:
0.497
Gnomad EAS
AF:
0.585
Gnomad SAS
AF:
0.415
Gnomad FIN
AF:
0.336
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.410
Gnomad OTH
AF:
0.447
GnomAD3 exomes
AF:
0.408
AC:
102506
AN:
251386
Hom.:
21805
AF XY:
0.413
AC XY:
56076
AN XY:
135862
show subpopulations
Gnomad AFR exome
AF:
0.376
Gnomad AMR exome
AF:
0.330
Gnomad ASJ exome
AF:
0.500
Gnomad EAS exome
AF:
0.593
Gnomad SAS exome
AF:
0.414
Gnomad FIN exome
AF:
0.327
Gnomad NFE exome
AF:
0.411
Gnomad OTH exome
AF:
0.413
GnomAD4 exome
AF:
0.408
AC:
595959
AN:
1461692
Hom.:
123250
AF XY:
0.410
AC XY:
298131
AN XY:
727156
show subpopulations
Gnomad4 AFR exome
AF:
0.378
Gnomad4 AMR exome
AF:
0.336
Gnomad4 ASJ exome
AF:
0.501
Gnomad4 EAS exome
AF:
0.541
Gnomad4 SAS exome
AF:
0.420
Gnomad4 FIN exome
AF:
0.323
Gnomad4 NFE exome
AF:
0.406
Gnomad4 OTH exome
AF:
0.427
Alfa
AF:
0.419
Hom.:
32640
Bravo
AF:
0.403
Asia WGS
AF:
0.490
AC:
1705
AN:
3478
EpiCase
AF:
0.429
EpiControl
AF:
0.445

ClinVar

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

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 09, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
Cadd
Benign
6.3
Dann
Benign
0.60

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: rs6313; hg19: chr13-47469940; COSMIC: COSV66327259; API