rs4495839

Positions:

• chr10-46314592-A-G
• chr10-46314592-A-T

Variant summary

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

The NM_001278688.3(ANTXRL):​c.1410+1276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,292 control chromosomes in the GnomAD database, including 14,110 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 0.44 (14110 hom., cov: 31)
• Consequence: ANTXRL NM_001278688.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANTXRL	NM_001278688.3	c.1410+1276A>G		intron_variant		ENST00000620264.5	NP_001265617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANTXRL	ENST00000620264.5	c.1410+1276A>G		intron_variant		5	NM_001278688.3	ENSP00000480615	P1
ANTXRL	ENST00000617088.4	c.*560+1276A>G		intron_variant, NMD_transcript_variant		5		ENSP00000481410

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66209 AN: 151174 Hom.: 14103 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.438 AC: 66267 AN: 151292 Hom.: 14110 Cov.: 31 AF XY: 0.435 AC XY: 32134 AN XY: 73894

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.447

Alfa AF: 0.469 Hom.: 14881

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.50

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: rs4495839; hg19: chr10-47685828;