10-46325790-C-T

Variant names:

• chr10-46325790-C-T
• rs4466762
• NM_001278688.3:c.1411-3809C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278688.3(ANTXRL):​c.1411-3809C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,744 control chromosomes in the GnomAD database, including 21,291 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 0.52 (21291 hom., cov: 32)
• Consequence: ANTXRL NM_001278688.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 3 publications found

Genes affected

ANTXRL (HGNC:27277): (ANTXR like) Predicted to enable transmembrane signaling receptor activity. Predicted to be involved in toxin transport. Predicted to be integral component of membrane. Predicted to be active in cell surface and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278688.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTXRL	NM_001278688.3	MANE Select	c.1411-3809C>T		intron	N/A	NP_001265617.1
	ANTXRL	NM_001354208.2		c.517-3809C>T		intron	N/A	NP_001341137.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTXRL	ENST00000620264.5	TSL:5 MANE Select	c.1411-3809C>T		intron	N/A	ENSP00000480615.1
	ANTXRL	ENST00000617088.5	TSL:5	n.*561-3809C>T		intron	N/A	ENSP00000481410.1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78452 AN: 151626 Hom.: 21289 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.517 AC: 78492 AN: 151744 Hom.: 21291 Cov.: 32 AF XY: 0.520 AC XY: 38584 AN XY: 74134

African (AFR) AF: 0.288 AC: 11926 AN: 41374

American (AMR) AF: 0.631 AC: 9632 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2007 AN: 3462

East Asian (EAS) AF: 0.345 AC: 1780 AN: 5156

South Asian (SAS) AF: 0.475 AC: 2286 AN: 4810

European-Finnish (FIN) AF: 0.681 AC: 7152 AN: 10500

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41895 AN: 67870

Other (OTH) AF: 0.529 AC: 1115 AN: 2108

Alfa AF: 0.584 Hom.: 11376

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4466762; hg19: chr10-47697026;