rs10885789

chr10-115719286-A-Cchr10-115719286-A-Gchr10-115719286-A-T

Variant summary

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

The NM_207303.4(ATRNL1):c.3796-7962A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,906 control chromosomes in the GnomAD database, including 17,299 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 0.47 (17299 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.3796-7962A>C		intron_variant		ENST00000355044.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3796-7962A>C		intron_variant		1	NM_207303.4	P1
ATRNL1	ENST00000650603.1	c.3688-7962A>C		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70610 AN: 151788 Hom.: 17264 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.465 AC: 70703 AN: 151906 Hom.: 17299 Cov.: 32 AF XY: 0.473 AC XY: 35144 AN XY: 74252

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.477

Alfa AF: 0.290 Hom.: 694

Bravo AF: 0.481

Asia WGS AF: 0.643 AC: 2233 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.68
Dann	Benign	0.74

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: rs10885789; hg19: chr10-117478796;