chr20-3567442-T-C

Variant names:

• chr20-3567442-T-C
• rs170977
• NM_139321.3:c.1871+2010T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139321.3(ATRN):​c.1871+2010T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,186 control chromosomes in the GnomAD database, including 48,832 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 0.80 (48832 hom., cov: 31)
• Consequence: ATRN NM_139321.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 0 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRN	NM_139321.3	c.1871+2010T>C		intron_variant	Intron 11 of 28	ENST00000262919.10	NP_647537.1
ATRN	NM_001323332.2	c.1871+2010T>C		intron_variant	Intron 11 of 25		NP_001310261.1
ATRN	NM_139322.4	c.1871+2010T>C		intron_variant	Intron 11 of 24		NP_647538.1
ATRN	NM_001207047.3	c.1523+2010T>C		intron_variant	Intron 11 of 24		NP_001193976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRN	ENST00000262919.10	c.1871+2010T>C		intron_variant	Intron 11 of 28	5	NM_139321.3	ENSP00000262919.5
ATRN	ENST00000446916.2	c.1871+2010T>C		intron_variant	Intron 11 of 24	1		ENSP00000416587.2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121402 AN: 152068 Hom.: 48791 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.798 AC: 121500 AN: 152186 Hom.: 48832 Cov.: 31 AF XY: 0.803 AC XY: 59766 AN XY: 74412

African (AFR) AF: 0.746 AC: 30933 AN: 41484

American (AMR) AF: 0.830 AC: 12696 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2650 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5185 AN: 5194

South Asian (SAS) AF: 0.912 AC: 4395 AN: 4820

European-Finnish (FIN) AF: 0.854 AC: 9046 AN: 10590

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53868 AN: 68018

Other (OTH) AF: 0.789 AC: 1666 AN: 2112

Alfa AF: 0.793 Hom.: 5872

Bravo AF: 0.792

Asia WGS AF: 0.952 AC: 3311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		-0.15
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: rs170977; hg19: chr20-3548089;