chr10-115753077-T-G

Position:

• chr10-115753077-T-G

Variant summary

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

The NM_207303.4(ATRNL1):​c.3903+25722T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,804 control chromosomes in the GnomAD database, including 18,344 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 (18344 hom., cov: 31)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3903+25722T>G		intron_variant		ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3903+25722T>G		intron_variant		1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000650603.1	n.3795+25722T>G		intron_variant				ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71057 AN: 151686 Hom.: 18338 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.468 AC: 71077 AN: 151804 Hom.: 18344 Cov.: 31 AF XY: 0.473 AC XY: 35104 AN XY: 74170

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.511

Alfa AF: 0.503 Hom.: 9854

Bravo AF: 0.466

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.66

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: rs10490919; hg19: chr10-117512588;