20-3544872-C-T

Position:

• chr20-3544872-C-T

Variant summary

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

The NM_139321.3(ATRN):​c.609-890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.963 in 150,408 control chromosomes in the GnomAD database, including 69,727 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 0.96 (69727 hom., cov: 24)
• Consequence: ATRN NM_139321.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRN	NM_139321.3	c.609-890C>T		intron_variant		ENST00000262919.10	NP_647537.1
ATRN	NM_001207047.3	c.261-890C>T		intron_variant			NP_001193976.1
ATRN	NM_001323332.2	c.609-890C>T		intron_variant			NP_001310261.1
ATRN	NM_139322.4	c.609-890C>T		intron_variant			NP_647538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATRN	ENST00000262919.10	c.609-890C>T		intron_variant		5	NM_139321.3	ENSP00000262919	P2
ATRN	ENST00000446916.2	c.609-890C>T		intron_variant		1		ENSP00000416587	A2

Frequencies

GnomAD3 genomes AF: 0.963 AC: 144683 AN: 150316 Hom.: 69684 Cov.: 24

Gnomad AFR AF: 0.990

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.963 AC: 144772 AN: 150408 Hom.: 69727 Cov.: 24 AF XY: 0.961 AC XY: 70496 AN XY: 73368

Gnomad4 AFR AF: 0.990

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.971

Alfa AF: 0.954 Hom.: 13636

Bravo AF: 0.970

Asia WGS AF: 0.968 AC: 3362 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.77

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: rs151507; hg19: chr20-3525519;