20-3553693-G-A

Variant names:

• chr20-3553693-G-A
• rs235590
• NM_139321.3:c.1112+4355G>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.1112+4355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,194 control chromosomes in the GnomAD database, including 53,969 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 0.84 (53969 hom., cov: 31)
• Consequence: ATRN NM_139321.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.1112+4355G>A		intron	N/A	NP_647537.1
	ATRN	NM_001323332.2		c.1112+4355G>A		intron	N/A	NP_001310261.1
	ATRN	NM_139322.4		c.1112+4355G>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.1112+4355G>A		intron	N/A	ENSP00000262919.5
	ATRN	ENST00000446916.2	TSL:1	c.1112+4355G>A		intron	N/A	ENSP00000416587.2

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127716 AN: 152076 Hom.: 53907 Cov.: 31

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.840 AC: 127835 AN: 152194 Hom.: 53969 Cov.: 31 AF XY: 0.845 AC XY: 62843 AN XY: 74394

African (AFR) AF: 0.871 AC: 36172 AN: 41518

American (AMR) AF: 0.851 AC: 13009 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2681 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5172 AN: 5180

South Asian (SAS) AF: 0.950 AC: 4571 AN: 4814

European-Finnish (FIN) AF: 0.858 AC: 9095 AN: 10596

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54310 AN: 68004

Other (OTH) AF: 0.825 AC: 1743 AN: 2114

Alfa AF: 0.828 Hom.: 8831

Bravo AF: 0.839

Asia WGS AF: 0.979 AC: 3403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.32
DANN	Benign	0.38
PhyloP100		-1.2
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: rs235590; hg19: chr20-3534340;