rs1264781

chr10-115123030-G-Achr10-115123030-G-C

Variant summary

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

The NM_207303.4(ATRNL1):c.491+1218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,030 control chromosomes in the GnomAD database, including 38,728 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 0.70 (38728 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.491+1218G>A		intron_variant		ENST00000355044.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.491+1218G>A		intron_variant		1	NM_207303.4	P1

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106899 AN: 151914 Hom.: 38692 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.704 AC: 106973 AN: 152030 Hom.: 38728 Cov.: 32 AF XY: 0.690 AC XY: 51299 AN XY: 74320

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.721

Alfa AF: 0.674 Hom.: 3526

Bravo AF: 0.702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1264781; hg19: chr10-116882794;