10-115379418-G-C

Position:

• chr10-115379418-G-C

Variant summary

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

The NM_207303.4(ATRNL1):​c.3176-15241G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,792 control chromosomes in the GnomAD database, including 11,458 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 0.37 (11458 hom., cov: 33)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRNL1	NM_207303.4	c.3176-15241G>C		intron_variant		ENST00000355044.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRNL1	ENST00000355044.8	c.3176-15241G>C		intron_variant		1	NM_207303.4	P1
ATRNL1	ENST00000526373.1	c.426-15241G>C		intron_variant		5
ATRNL1	ENST00000650603.1	c.3068-15241G>C		intron_variant, NMD_transcript_variant
ATRNL1	ENST00000534530.5	n.291-15241G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55714 AN: 151678 Hom.: 11432 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.367 AC: 55779 AN: 151792 Hom.: 11458 Cov.: 33 AF XY: 0.361 AC XY: 26789 AN XY: 74166

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.352

Alfa AF: 0.218 Hom.: 474

Bravo AF: 0.370

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.30

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: rs693986; hg19: chr10-117138928;