chr3-151880738-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_033050.6(SUCNR1):​c.195C>T​(p.Leu65Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,614,080 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 31 hom. )

Consequence

SUCNR1
NM_033050.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.367
Variant links:
Genes affected
SUCNR1 (HGNC:4542): (succinate receptor 1) This gene encodes a G-protein-coupled receptor for succinate, an intermediate molecule of the citric acid cycle. It is involved in the promotion of hematopoietic progenitor cell development, and it has a potential role in renovascular hypertension which has known correlations to renal failure, diabetes and atherosclerosis. [provided by RefSeq, Oct 2009]
AADACL2-AS1 (HGNC:50301): (AADACL2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 3-151880738-C-T is Benign according to our data. Variant chr3-151880738-C-T is described in ClinVar as [Benign]. Clinvar id is 713065.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.367 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00165 (251/152284) while in subpopulation EAS AF= 0.0374 (194/5188). AF 95% confidence interval is 0.0331. There are 3 homozygotes in gnomad4. There are 146 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SUCNR1NM_033050.6 linkc.195C>T p.Leu65Leu synonymous_variant Exon 3 of 3 ENST00000362032.6 NP_149039.2 Q9BXA5
AADACL2-AS1NR_110202.1 linkn.319+47119G>A intron_variant Intron 1 of 3
AADACL2-AS1NR_110203.1 linkn.319+47119G>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SUCNR1ENST00000362032.6 linkc.195C>T p.Leu65Leu synonymous_variant Exon 3 of 3 1 NM_033050.6 ENSP00000355156.4 Q9BXA5
AADACL2-AS1ENST00000475855.1 linkn.319+47119G>A intron_variant Intron 1 of 3 5
AADACL2-AS1ENST00000483843.6 linkn.439+36877G>A intron_variant Intron 2 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.00166
AC:
253
AN:
152166
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000965
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0375
Gnomad SAS
AF:
0.00703
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000220
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.00363
AC:
913
AN:
251284
Hom.:
15
AF XY:
0.00370
AC XY:
502
AN XY:
135814
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0400
Gnomad SAS exome
AF:
0.00392
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000361
Gnomad OTH exome
AF:
0.00212
GnomAD4 exome
AF:
0.00144
AC:
2103
AN:
1461796
Hom.:
31
Cov.:
33
AF XY:
0.00160
AC XY:
1162
AN XY:
727200
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0354
Gnomad4 SAS exome
AF:
0.00432
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000168
Gnomad4 OTH exome
AF:
0.00215
GnomAD4 genome
AF:
0.00165
AC:
251
AN:
152284
Hom.:
3
Cov.:
32
AF XY:
0.00196
AC XY:
146
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0374
Gnomad4 SAS
AF:
0.00683
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.000945
Alfa
AF:
0.000194
Hom.:
0
Bravo
AF:
0.00182
Asia WGS
AF:
0.0210
AC:
74
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000415

ClinVar

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

Submissions by phenotype

not provided Benign:1
May 18, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
CADD
Benign
3.9
DANN
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs79888638; hg19: chr3-151598526; COSMIC: COSV62911979; API