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GeneBe

20-3471167-A-C

Variant summary

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

The NM_139321.3(ATRN):c.60A>C(p.Ala20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,504,300 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0011 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000075 ( 1 hom. )

Consequence

ATRN
NM_139321.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.05
Variant links:
Genes affected
ATRN (HGNC:885): (attractin) This gene encodes both membrane-bound and secreted protein isoforms. A membrane-bound isoform exhibits sequence similarity with the mouse mahogany protein, a receptor involved in controlling obesity. A secreted isoform is involved in the initial immune cell clustering during inflammatory responses that may regulate the chemotactic activity of chemokines. [provided by RefSeq, Apr 2016]

Genome browser will be placed here

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=-0.7).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 20-3471167-A-C is Benign according to our data. Variant chr20-3471167-A-C is described in ClinVar as [Benign]. Clinvar id is 2057356.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=1.05 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 AC in GnomAd at 163 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATRNNM_139321.3 linkuse as main transcriptc.60A>C p.Ala20= synonymous_variant 1/29 ENST00000262919.10
ATRNNM_001323332.2 linkuse as main transcriptc.60A>C p.Ala20= synonymous_variant 1/26
ATRNNM_139322.4 linkuse as main transcriptc.60A>C p.Ala20= synonymous_variant 1/25
ATRNNM_001207047.3 linkuse as main transcriptc.62+33A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATRNENST00000262919.10 linkuse as main transcriptc.60A>C p.Ala20= synonymous_variant 1/295 NM_139321.3 P2O75882-1
ATRNENST00000446916.2 linkuse as main transcriptc.60A>C p.Ala20= synonymous_variant 1/251 A2O75882-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00107
AC:
163
AN:
151932
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00384
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.0000591
AC:
6
AN:
101502
Hom.:
0
AF XY:
0.0000352
AC XY:
2
AN XY:
56742
show subpopulations
Gnomad AFR exome
AF:
0.00191
Gnomad AMR exome
AF:
0.0000943
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000754
AC:
102
AN:
1352260
Hom.:
1
Cov.:
33
AF XY:
0.0000660
AC XY:
44
AN XY:
666952
show subpopulations
Gnomad4 AFR exome
AF:
0.00287
Gnomad4 AMR exome
AF:
0.000121
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000282
Gnomad4 OTH exome
AF:
0.000266
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00107
AC:
163
AN:
152040
Hom.:
1
Cov.:
33
AF XY:
0.000955
AC XY:
71
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.00383
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.000475
Alfa
AF:
0.000524
Hom.:
0
Bravo
AF:
0.00117
Asia WGS
AF:
0.000291
AC:
1
AN:
3448

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 testingInvitaeNov 06, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
Cadd
Benign
12
Dann
Benign
0.59
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs559292386; hg19: chr20-3451814; API