rs2024179

chr10-115831570-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.3904-16307A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,040 control chromosomes in the GnomAD database, including 2,215 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 0.16 (2215 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.3904-16307A>G		intron_variant		ENST00000355044.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3904-16307A>G		intron_variant		1	NM_207303.4	P1
ATRNL1	ENST00000650603.1	c.3796-16307A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24745 AN: 151922 Hom.: 2216 Cov.: 31

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.163 AC: 24744 AN: 152040 Hom.: 2215 Cov.: 31 AF XY: 0.162 AC XY: 12020 AN XY: 74314

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0347

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.177

Alfa AF: 0.191 Hom.: 2946

Bravo AF: 0.155

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.4
Dann	Benign	0.48

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: rs2024179; hg19: chr10-117591081;