10-115774009-C-T

Variant names:

• chr10-115774009-C-T
• rs10490917
• NM_207303.4:c.3903+46654C>T

Variant summary

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

The NM_207303.4(ATRNL1):​c.3903+46654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,016 control chromosomes in the GnomAD database, including 50,019 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 0.81 (50019 hom., cov: 30)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3903+46654C>T		intron_variant	Intron 27 of 28	ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3903+46654C>T		intron_variant	Intron 27 of 28	1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000650603.1	n.3795+46654C>T		intron_variant	Intron 27 of 29			ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123053 AN: 151898 Hom.: 49988 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.810 AC: 123137 AN: 152016 Hom.: 50019 Cov.: 30 AF XY: 0.811 AC XY: 60262 AN XY: 74276

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.799

Alfa AF: 0.808 Hom.: 6211

Bravo AF: 0.817

Asia WGS AF: 0.855 AC: 2973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.25

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: rs10490917; hg19: chr10-117533520;