20-3545054-G-A

Variant names:

• chr20-3545054-G-A
• rs238688
• NM_139321.3:c.609-708G>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.609-708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,818 control chromosomes in the GnomAD database, including 5,127 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 0.25 (5127 hom., cov: 31)
• Consequence: ATRN NM_139321.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRN	NM_139321.3	MANE Select	c.609-708G>A		intron	N/A	NP_647537.1	O75882-1
	ATRN	NM_001323332.2		c.609-708G>A		intron	N/A	NP_001310261.1
	ATRN	NM_139322.4		c.609-708G>A		intron	N/A	NP_647538.1	O75882-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRN	ENST00000262919.10	TSL:5 MANE Select	c.609-708G>A		intron	N/A	ENSP00000262919.5	O75882-1
	ATRN	ENST00000446916.2	TSL:1	c.609-708G>A		intron	N/A	ENSP00000416587.2	O75882-2
	ATRN	ENST00000928835.1		c.609-2230G>A		intron	N/A	ENSP00000598894.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37712 AN: 151704 Hom.: 5123 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.249 AC: 37734 AN: 151818 Hom.: 5127 Cov.: 31 AF XY: 0.243 AC XY: 18048 AN XY: 74218

African (AFR) AF: 0.288 AC: 11922 AN: 41404

American (AMR) AF: 0.216 AC: 3302 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5178

South Asian (SAS) AF: 0.103 AC: 499 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2171 AN: 10448

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18120 AN: 67934

Other (OTH) AF: 0.264 AC: 554 AN: 2102

Alfa AF: 0.155 Hom.: 324

Bravo AF: 0.253

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		0.33
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: rs238688; hg19: chr20-3525701;