rs1157117

Positions:

• chr10-115772880-G-A

Variant summary

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

The NM_207303.4(ATRNL1):​c.3903+45525G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,898 control chromosomes in the GnomAD database, including 18,039 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 0.46 (18039 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3903+45525G>A		intron_variant		ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3903+45525G>A		intron_variant		1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000650603.1	n.3795+45525G>A		intron_variant				ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70221 AN: 151780 Hom.: 18028 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.462 AC: 70246 AN: 151898 Hom.: 18039 Cov.: 31 AF XY: 0.467 AC XY: 34668 AN XY: 74200

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.509

Alfa AF: 0.506 Hom.: 8527

Bravo AF: 0.459

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.43

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: rs1157117; hg19: chr10-117532391;