chr10-115508172-C-T

Position:

• chr10-115508172-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.3655-11091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 151,816 control chromosomes in the GnomAD database, including 39,452 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 0.71 (39452 hom., cov: 32)
• Consequence: ATRNL1 NM_207303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATRNL1	NM_207303.4	c.3655-11091C>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.3655-11091C>T		intron_variant		1	NM_207303.4	ENSP00000347152	P1
ATRNL1	ENST00000650603.1	c.3547-11091C>T		intron_variant, NMD_transcript_variant				ENSP00000497485
ATRNL1	ENST00000424738.1	n.238-11091C>T		intron_variant, non_coding_transcript_variant		3
ATRNL1	ENST00000534530.5	n.438-11091C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107679 AN: 151698 Hom.: 39421 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.710 AC: 107757 AN: 151816 Hom.: 39452 Cov.: 32 AF XY: 0.698 AC XY: 51738 AN XY: 74150

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.718

Alfa AF: 0.728 Hom.: 5064

Bravo AF: 0.707

Asia WGS AF: 0.470 AC: 1637 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.48

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: rs1336119; hg19: chr10-117267682;