rs1017822

Positions:

• chr10-115882066-C-G
• chr10-115882066-C-T

Variant summary

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

The NM_207303.4(ATRNL1):​c.4018+34075C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,036 control chromosomes in the GnomAD database, including 23,356 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 0.54 (23356 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.4018+34075C>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.4018+34075C>G		intron_variant		1	NM_207303.4	ENSP00000347152.3
ATRNL1	ENST00000650603.1	n.3910+34075C>G		intron_variant				ENSP00000497485.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81592 AN: 151918 Hom.: 23353 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.537 AC: 81615 AN: 152036 Hom.: 23356 Cov.: 32 AF XY: 0.542 AC XY: 40252 AN XY: 74298

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.568

Alfa AF: 0.563 Hom.: 3102

Bravo AF: 0.529

Asia WGS AF: 0.610 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.35
DANN	Benign	0.40

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: rs1017822; hg19: chr10-117641577;