rs2804147

Positions:

• chr10-115679524-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.3796-47724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,904 control chromosomes in the GnomAD database, including 4,947 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 0.25 (4947 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

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 = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.3796-47724A>G		intron_variant		ENST00000355044.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3796-47724A>G		intron_variant		1	NM_207303.4	P1
ATRNL1	ENST00000650603.1	c.3688-47724A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37470 AN: 151786 Hom.: 4947 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.247 AC: 37487 AN: 151904 Hom.: 4947 Cov.: 31 AF XY: 0.246 AC XY: 18223 AN XY: 74212

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.243

Alfa AF: 0.266 Hom.: 4205

Bravo AF: 0.240

Asia WGS AF: 0.272 AC: 948 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	0.81
DANN	Benign	0.55

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: rs2804147; hg19: chr10-117439034;