rs237640

Positions:

• chr20-3563569-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139321.3(ATRN):​c.1786+206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,094 control chromosomes in the GnomAD database, including 3,458 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3458 hom., cov: 32)
• Consequence: ATRN NM_139321.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRN	NM_139321.3	c.1786+206G>A		intron_variant		ENST00000262919.10
ATRN	NM_001207047.3	c.1438+206G>A		intron_variant
ATRN	NM_001323332.2	c.1786+206G>A		intron_variant
ATRN	NM_139322.4	c.1786+206G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRN	ENST00000262919.10	c.1786+206G>A		intron_variant		5	NM_139321.3	P2
ATRN	ENST00000446916.2	c.1786+206G>A		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30803 AN: 151976 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.214

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.203 AC: 30824 AN: 152094 Hom.: 3458 Cov.: 32 AF XY: 0.198 AC XY: 14701 AN XY: 74362

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.211

Alfa AF: 0.205 Hom.: 666

Bravo AF: 0.209

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs237640; hg19: chr20-3544216;