rs2907582

chr10-115789516-G-Achr10-115789516-G-Cchr10-115789516-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.3904-58361G>A		intron_variant		ENST00000355044.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3904-58361G>A		intron_variant		1	NM_207303.4	P1
ATRNL1	ENST00000650603.1	c.3796-58361G>A		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.804

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	0.089
Dann	Benign	0.70

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: rs2907582; hg19: chr10-117549027;