rs17354968

chr10-115917623-T-C

Variant summary

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

The NM_207303.4(ATRNL1):c.4019-27035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,170 control chromosomes in the GnomAD database, including 2,392 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 0.16 (2392 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

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]

LOC105378497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.4019-27035T>C		intron_variant		ENST00000355044.8
LOC105378497	XR_001747597.3	n.68+1460A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.4019-27035T>C		intron_variant		1	NM_207303.4	P1
ATRNL1	ENST00000650603.1	c.3911-13905T>C		intron_variant, NMD_transcript_variant
ATRNL1	ENST00000449616.2	n.227+8046T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24830 AN: 152052 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.163 AC: 24819 AN: 152170 Hom.: 2392 Cov.: 32 AF XY: 0.161 AC XY: 11945 AN XY: 74380

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.167

Alfa AF: 0.178 Hom.: 428

Bravo AF: 0.157

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	2.5
Dann	Benign	0.82

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: rs17354968; hg19: chr10-117677134;