10-115148713-C-T

Variant names:

• chr10-115148713-C-T
• rs1314595
• NM_207303.4:c.830-11327C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.830-11327C>T		intron_variant	Intron 5 of 28	ENST00000355044.8	NP_997186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATRNL1	ENST00000355044.8	c.830-11327C>T		intron_variant	Intron 5 of 28	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

African (AFR) AF: 0.141 AC: 5742 AN: 40652

American (AMR) AF: 0.0154 AC: 231 AN: 14998

Ashkenazi Jewish (ASJ) AF: 0.00290 AC: 10 AN: 3446

East Asian (EAS) AF: 0.000197 AC: 1 AN: 5086

South Asian (SAS) AF: 0.000428 AC: 2 AN: 4676

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9538

Middle Eastern (MID) AF: 0.0250 AC: 7 AN: 280

European-Non Finnish (NFE) AF: 0.000680 AC: 46 AN: 67624

Other (OTH) AF: 0.0310 AC: 64 AN: 2066

Alfa AF: 0.0167 Hom.: 75

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
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs1314595; hg19: chr10-116908479;