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GeneBe

7-150338988-G-T

Variant summary

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

The NM_002889.4(RARRES2):c.373C>A(p.Arg125=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00555 in 1,602,528 control chromosomes in the GnomAD database, including 371 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 205 hom., cov: 32)
Exomes 𝑓: 0.0031 ( 166 hom. )

Consequence

RARRES2
NM_002889.4 splice_region, synonymous

Scores

2
Splicing: ADA: 0.001769
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.47
Variant links:
Genes affected
RARRES2 (HGNC:9868): (retinoic acid receptor responder 2) This gene encodes a secreted chemotactic protein that initiates chemotaxis via the ChemR23 G protein-coupled seven-transmembrane domain ligand. Expression of this gene is upregulated by the synthetic retinoid tazarotene and occurs in a wide variety of tissues. The active protein has several roles, including that as an adipokine and as an antimicrobial protein with activity against bacteria and fungi. [provided by RefSeq, Nov 2014]

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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=-0.81).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-150338988-G-T is Benign according to our data. Variant chr7-150338988-G-T is described in ClinVar as [Benign]. Clinvar id is 776268.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=1.47 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0978 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RARRES2NM_002889.4 linkuse as main transcriptc.373C>A p.Arg125= splice_region_variant, synonymous_variant 4/6 ENST00000223271.8
RARRES2XR_007060121.1 linkuse as main transcriptn.445C>A splice_region_variant, non_coding_transcript_exon_variant 4/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RARRES2ENST00000223271.8 linkuse as main transcriptc.373C>A p.Arg125= splice_region_variant, synonymous_variant 4/61 NM_002889.4 P1
ENST00000647589.1 linkuse as main transcriptn.117+1389G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0288
AC:
4373
AN:
152070
Hom.:
205
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.100
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0101
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.0230
GnomAD3 exomes
AF:
0.00749
AC:
1883
AN:
251264
Hom.:
86
AF XY:
0.00516
AC XY:
700
AN XY:
135788
show subpopulations
Gnomad AFR exome
AF:
0.101
Gnomad AMR exome
AF:
0.00451
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000431
Gnomad OTH exome
AF:
0.00604
GnomAD4 exome
AF:
0.00311
AC:
4507
AN:
1450340
Hom.:
166
Cov.:
31
AF XY:
0.00271
AC XY:
1960
AN XY:
722268
show subpopulations
Gnomad4 AFR exome
AF:
0.103
Gnomad4 AMR exome
AF:
0.00501
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000291
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000336
Gnomad4 OTH exome
AF:
0.00681
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0289
AC:
4394
AN:
152188
Hom.:
205
Cov.:
32
AF XY:
0.0280
AC XY:
2081
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.100
Gnomad4 AMR
AF:
0.0101
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.0227
Alfa
AF:
0.00184
Hom.:
19
Bravo
AF:
0.0325
Asia WGS
AF:
0.0100
AC:
36
AN:
3478
EpiCase
AF:
0.000436
EpiControl
AF:
0.000711

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 testingInvitaeAug 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
7.1
Dann
Benign
0.73
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.0

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0018
dbscSNV1_RF
Benign
0.096
SpliceAI score (max)
0.030
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: rs1804764; hg19: chr7-150036077; API