chr10-115148713-C-T

Position:

• chr10-115148713-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.830-11327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 149,272 control chromosomes in the GnomAD database, including 424 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 0.041 (424 hom., cov: 30)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

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]

ENSG00000285582 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.830-11327C>T		intron_variant		ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.830-11327C>T		intron_variant		1	NM_207303.4	ENSP00000347152.3

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6116 AN: 149246 Hom.: 425 Cov.: 30

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0265

Gnomad AMR AF: 0.0155

Gnomad ASJ AF: 0.00290

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.000639

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0197

Gnomad NFE AF: 0.000680

Gnomad OTH AF: 0.0312

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

GnomAD4 genome AF: 0.0410 AC: 6127 AN: 149272 Hom.: 424 Cov.: 30 AF XY: 0.0394 AC XY: 2859 AN XY: 72522

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0154

Gnomad4 ASJ AF: 0.00290

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.000428

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000680

Gnomad4 OTH AF: 0.0310

Alfa AF: 0.0165 Hom.: 63

Bravo AF: 0.0469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1314595; hg19: chr10-116908479;