10-115159858-A-G

Position:

• chr10-115159858-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.830-182A>G		intron_variant		ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.830-182A>G		intron_variant		1	NM_207303.4	ENSP00000347152.3

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

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.723

Alfa AF: 0.726 Hom.: 4723

Bravo AF: 0.697

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1264798; hg19: chr10-116919619;