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GeneBe

7-150340550-G-C

Variant summary

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

The NM_002889.4(RARRES2):c.60C>G(p.Ala20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 1,575,062 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 70 hom. )

Consequence

RARRES2
NM_002889.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.08
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=-0.86).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-150340550-G-C is Benign according to our data. Variant chr7-150340550-G-C is described in ClinVar as [Benign]. Clinvar id is 771419.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=-4.07 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00267 (406/152290) while in subpopulation AMR AF= 0.0192 (294/15302). AF 95% confidence interval is 0.0174. There are 7 homozygotes in gnomad4. There are 215 alleles in male gnomad4 subpopulation. Median coverage is 32. 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 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RARRES2NM_002889.4 linkuse as main transcriptc.60C>G p.Ala20= synonymous_variant 2/6 ENST00000223271.8
RARRES2XR_007060121.1 linkuse as main transcriptn.132C>G non_coding_transcript_exon_variant 2/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RARRES2ENST00000223271.8 linkuse as main transcriptc.60C>G p.Ala20= synonymous_variant 2/61 NM_002889.4 P1
ENST00000647589.1 linkuse as main transcriptn.118-1621G>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00265
AC:
404
AN:
152172
Hom.:
7
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000434
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0190
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0158
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00998
AC:
1799
AN:
180342
Hom.:
54
AF XY:
0.00768
AC XY:
752
AN XY:
97902
show subpopulations
Gnomad AFR exome
AF:
0.000997
Gnomad AMR exome
AF:
0.0551
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0161
Gnomad SAS exome
AF:
0.000359
Gnomad FIN exome
AF:
0.0000641
Gnomad NFE exome
AF:
0.000227
Gnomad OTH exome
AF:
0.00459
GnomAD4 exome
AF:
0.00206
AC:
2924
AN:
1422772
Hom.:
70
Cov.:
31
AF XY:
0.00188
AC XY:
1323
AN XY:
704696
show subpopulations
Gnomad4 AFR exome
AF:
0.000398
Gnomad4 AMR exome
AF:
0.0487
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0203
Gnomad4 SAS exome
AF:
0.000550
Gnomad4 FIN exome
AF:
0.0000206
Gnomad4 NFE exome
AF:
0.0000960
Gnomad4 OTH exome
AF:
0.00160
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00267
AC:
406
AN:
152290
Hom.:
7
Cov.:
32
AF XY:
0.00289
AC XY:
215
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.0192
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0157
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000285
Hom.:
0
Bravo
AF:
0.00472
Asia WGS
AF:
0.0110
AC:
37
AN:
3478

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 testingInvitaeJul 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
0.15
Dann
Benign
0.68
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs189776236; hg19: chr7-150037639; COSMIC: COSV56232194; COSMIC: COSV56232194; API