Variant 20-3471261-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_139321.3(ATRN):c.154C>T(p.Leu52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 1,448,050 control chromosomes in the GnomAD database, including 1,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.055 ( 726 hom., cov: 33)

Exomes 𝑓: 0.0078 ( 555 hom. )

Consequence

ATRN
NM_139321.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.316

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]

ATRN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 20-3471261-C-T is Benign according to our data. Variant chr20-3471261-C-T is described in ClinVar as [Benign]. Clinvar id is 1167763.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.316 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ATRN	NM_139321.3 linkuse as main transcript	c.154C>T	p.Leu52=	synonymous_variant	1/29	ENST00000262919.10
ATRN	NM_001323332.2 linkuse as main transcript	c.154C>T	p.Leu52=	synonymous_variant	1/26
ATRN	NM_139322.4 linkuse as main transcript	c.154C>T	p.Leu52=	synonymous_variant	1/25
ATRN	NM_001207047.3 linkuse as main transcript	c.62+127C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRN	ENST00000262919.10 linkuse as main transcript	c.154C>T	p.Leu52=	synonymous_variant	1/29	5	NM_139321.3	P2	O75882-1
ATRN	ENST00000446916.2 linkuse as main transcript	c.154C>T	p.Leu52=	synonymous_variant	1/25	1		A2	O75882-2

Frequencies

GnomAD3 genomes

AF:

0.0550

AC:

8370

AN:

152070

Hom.:

721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0219

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0337

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0541

Gnomad NFE

AF:

0.00240

Gnomad OTH

AF:

0.0455

GnomAD3 exomes

AF:

0.0139

AC:

687

AN:

49504

Hom.:

AF XY:

0.0143

AC XY:

413

AN XY:

28796

show subpopulations

Gnomad AFR exome

AF:

0.190

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.000277

Gnomad EAS exome

AF:

0.000485

Gnomad SAS exome

AF:

0.0367

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00288

Gnomad OTH exome

AF:

0.0135

GnomAD4 exome

AF:

0.00777

AC:

10066

AN:

1295872

Hom.:

555

Cov.:

AF XY:

0.00802

AC XY:

5107

AN XY:

637104

show subpopulations

Gnomad4 AFR exome

AF:

0.190

Gnomad4 AMR exome

AF:

0.0133

Gnomad4 ASJ exome

AF:

0.000192

Gnomad4 EAS exome

AF:

0.0000349

Gnomad4 SAS exome

AF:

0.0350

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00148

Gnomad4 OTH exome

AF:

0.0165

GnomAD4 genome

AF:

0.0552

AC:

8404

AN:

152178

Hom.:

726

Cov.:

AF XY:

0.0538

AC XY:

4007

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.0219

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0337

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00240

Gnomad4 OTH

AF:

0.0450

Alfa

AF:

0.00810

Hom.:

Bravo

AF:

0.0623

Asia WGS

AF:

0.0260

AC:

AN:

3460

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -

ATRN-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 30, 2024

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.7

DANN

Benign

0.89

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over