chr20-3563569-G-A

Variant names:

• chr20-3563569-G-A
• rs237640
• NM_139321.3:c.1786+206G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139321.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRN	NM_139321.3	MANE Select	c.1786+206G>A		intron	N/A	NP_647537.1
	ATRN	NM_001323332.2		c.1786+206G>A		intron	N/A	NP_001310261.1
	ATRN	NM_139322.4		c.1786+206G>A		intron	N/A	NP_647538.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRN	ENST00000262919.10	TSL:5 MANE Select	c.1786+206G>A		intron	N/A	ENSP00000262919.5
	ATRN	ENST00000446916.2	TSL:1	c.1786+206G>A		intron	N/A	ENSP00000416587.2

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

African (AFR) AF: 0.258 AC: 10695 AN: 41460

American (AMR) AF: 0.170 AC: 2601 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0885 AC: 427 AN: 4824

European-Finnish (FIN) AF: 0.146 AC: 1541 AN: 10572

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14139 AN: 67990

Other (OTH) AF: 0.211 AC: 446 AN: 2110

Alfa AF: 0.206 Hom.: 701

Bravo AF: 0.209

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.45
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs237640; hg19: chr20-3544216;