NM_207303.4:c.830-182A>G

Variant names:

• chr10-115159858-A-G
• rs1264798
• NM_207303.4:c.830-182A>G

Variant summary

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

The NM_207303.4(ATRNL1):​c.830-182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,404 control chromosomes in the GnomAD database, including 38,605 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 0.71 (38605 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 1 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]

ENSG00000285582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	NM_207303.4	MANE Select	c.830-182A>G		intron	N/A	NP_997186.1
	ATRNL1	NM_001276282.4		c.830-182A>G		intron	N/A	NP_001263211.1
	ATRNL1	NR_074088.3		n.1106-182A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	ENST00000355044.8	TSL:1 MANE Select	c.830-182A>G		intron	N/A	ENSP00000347152.3
	ATRNL1	ENST00000609571.5	TSL:1	c.830-182A>G		intron	N/A	ENSP00000476902.2
	ATRNL1	ENST00000527407.5	TSL:5	c.830-182A>G		intron	N/A	ENSP00000473412.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 106860 AN: 151286 Hom.: 38580 Cov.: 31

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.706 AC: 106921 AN: 151404 Hom.: 38605 Cov.: 31 AF XY: 0.694 AC XY: 51355 AN XY: 73962

African (AFR) AF: 0.764 AC: 31604 AN: 41380

American (AMR) AF: 0.562 AC: 8512 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2662 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5170

South Asian (SAS) AF: 0.631 AC: 3040 AN: 4820

European-Finnish (FIN) AF: 0.633 AC: 6627 AN: 10466

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50463 AN: 67654

Other (OTH) AF: 0.723 AC: 1519 AN: 2100

Alfa AF: 0.727 Hom.: 4949

Bravo AF: 0.697

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1264798; hg19: chr10-116919619;