rs2907582

Variant names:

• chr10-115789516-G-A
• rs2907582
• NM_207303.4:c.3904-58361G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-115789516-G-A
• chr10-115789516-G-C
• chr10-115789516-G-T

Variant summary

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

The NM_207303.4(ATRNL1):​c.3904-58361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,094 control chromosomes in the GnomAD database, including 44,705 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 0.77 (44705 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 0 publications found

Genes affected

ATRNL1 (HGNC:29063): (attractin like 1) Predicted to enable carbohydrate binding activity. Predicted to be involved in several processes, including animal organ morphogenesis; cell migration; and substrate adhesion-dependent cell spreading. Predicted to act upstream of or within G protein-coupled receptor signaling pathway. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in basement membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207303.4. 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
	ATRNL1	NM_207303.4	MANE Select	c.3904-58361G>A		intron	N/A	NP_997186.1	Q4G0Y2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	ENST00000355044.8	TSL:1 MANE Select	c.3904-58361G>A		intron	N/A	ENSP00000347152.3	Q5VV63-1
	ATRNL1	ENST00000943847.1		c.3685-58361G>A		intron	N/A	ENSP00000613906.1
	ATRNL1	ENST00000650603.1		n.3796-58361G>A		intron	N/A	ENSP00000497485.1	A0A3B3ISV6

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116407 AN: 151976 Hom.: 44665 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.766 AC: 116505 AN: 152094 Hom.: 44705 Cov.: 32 AF XY: 0.766 AC XY: 56981 AN XY: 74342

African (AFR) AF: 0.791 AC: 32818 AN: 41474

American (AMR) AF: 0.826 AC: 12615 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2615 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4181 AN: 5170

South Asian (SAS) AF: 0.701 AC: 3377 AN: 4818

European-Finnish (FIN) AF: 0.758 AC: 8014 AN: 10572

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50234 AN: 67996

Other (OTH) AF: 0.804 AC: 1697 AN: 2112

Alfa AF: 0.750 Hom.: 5318

Bravo AF: 0.775

Asia WGS AF: 0.788 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.089
DANN	Benign	0.70
PhyloP100		-0.39
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: rs2907582; hg19: chr10-117549027;