NM_001278688.3:c.1410+1276A>G

Variant names:

• chr10-46314592-A-G
• rs4495839
• NM_001278688.3:c.1410+1276A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.92).
• 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 rank	MANE	Protein	UniProt
ANTXRL	NM_001278688.3	c.1410+1276A>G		intron_variant	Intron 16 of 16	ENST00000620264.5	NP_001265617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANTXRL	ENST00000620264.5	c.1410+1276A>G		intron_variant	Intron 16 of 16	5	NM_001278688.3	ENSP00000480615.1
ANTXRL	ENST00000617088.5	n.*560+1276A>G		intron_variant	Intron 18 of 19	5		ENSP00000481410.1

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

African (AFR) AF: 0.386 AC: 15887 AN: 41206

American (AMR) AF: 0.482 AC: 7321 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1580 AN: 3456

East Asian (EAS) AF: 0.200 AC: 1020 AN: 5098

South Asian (SAS) AF: 0.343 AC: 1649 AN: 4806

European-Finnish (FIN) AF: 0.474 AC: 4969 AN: 10482

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.478 AC: 32395 AN: 67742

Other (OTH) AF: 0.447 AC: 943 AN: 2110

Alfa AF: 0.460 Hom.: 28150

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
PhyloP100		0.80
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: rs4495839; hg19: chr10-47685828;