chr10-115772880-G-A

Variant names:

• chr10-115772880-G-A
• rs1157117
• NM_207303.4:c.3903+45525G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.3903+45525G>A		intron	N/A	NP_997186.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	ENST00000355044.8	TSL:1 MANE Select	c.3903+45525G>A		intron	N/A	ENSP00000347152.3
	ATRNL1	ENST00000650603.1		n.3795+45525G>A		intron	N/A	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

African (AFR) AF: 0.226 AC: 9337 AN: 41402

American (AMR) AF: 0.594 AC: 9084 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2090 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3548 AN: 5166

South Asian (SAS) AF: 0.457 AC: 2205 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5623 AN: 10500

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36648 AN: 67944

Other (OTH) AF: 0.509 AC: 1071 AN: 2106

Alfa AF: 0.506 Hom.: 9664

Bravo AF: 0.459

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1157117; hg19: chr10-117532391;