rs7895458

Positions:

• chr10-46290653-G-C
• chr10-46290653-G-T

Variant summary

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

The NM_001278688.3(ANTXRL):​c.249-1405G>C 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 151,964 control chromosomes in the GnomAD database, including 21,592 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 (21592 hom., cov: 34)
• Consequence: ANTXRL NM_001278688.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANTXRL	NM_001278688.3	c.249-1405G>C		intron_variant		ENST00000620264.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANTXRL	ENST00000620264.5	c.249-1405G>C		intron_variant		5	NM_001278688.3	P1
ANTXRL	ENST00000619553.4	c.-37-1405G>C		intron_variant		4
ANTXRL	ENST00000617088.4	c.-37-1405G>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78522 AN: 151846 Hom.: 21585 Cov.: 34

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.517 AC: 78547 AN: 151964 Hom.: 21592 Cov.: 34 AF XY: 0.514 AC XY: 38166 AN XY: 74276

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.531

Alfa AF: 0.450 Hom.: 1280

Asia WGS AF: 0.340 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.082
DANN	Benign	0.31

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: rs7895458; hg19: chr10-47661889;