10-115679524-A-G

Variant names:

• chr10-115679524-A-G
• rs2804147
• NM_207303.4:c.3796-47724A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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 = 0.369 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	NM_207303.4	MANE Select	c.3796-47724A>G		intron	N/A	NP_997186.1	Q4G0Y2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATRNL1	ENST00000355044.8	TSL:1 MANE Select	c.3796-47724A>G		intron	N/A	ENSP00000347152.3	Q5VV63-1
	ATRNL1	ENST00000943847.1		c.3577-47724A>G		intron	N/A	ENSP00000613906.1
	ATRNL1	ENST00000650603.1		n.3688-47724A>G		intron	N/A	ENSP00000497485.1	A0A3B3ISV6

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

African (AFR) AF: 0.188 AC: 7810 AN: 41458

American (AMR) AF: 0.178 AC: 2708 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3464

East Asian (EAS) AF: 0.383 AC: 1963 AN: 5130

South Asian (SAS) AF: 0.281 AC: 1352 AN: 4806

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19470 AN: 67918

Other (OTH) AF: 0.243 AC: 512 AN: 2110

Alfa AF: 0.270 Hom.: 15640

Bravo AF: 0.240

Asia WGS AF: 0.272 AC: 948 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	0.81
DANN	Benign	0.55
PhyloP100		-0.84
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: rs2804147; hg19: chr10-117439034;