ENST00000617088.5:n.*1226A>G

Variant names:

• chr10-46330334-A-G
• rs11596854
• ENST00000617088.5:n.*1226A>G

Variant summary

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

The ENST00000617088.5(ANTXRL):​n.*1226A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 515,298 control chromosomes in the GnomAD database, including 35,878 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 0.34 (9596 hom., cov: 33)
  • Exomes 𝑓: 0.38 (26282 hom.)
• Consequence: ANTXRL ENST00000617088.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.850
• Publications: 2 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 = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANTXRL	NM_001278688.3	c.*250A>G		downstream_gene_variant		ENST00000620264.5	NP_001265617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANTXRL	ENST00000617088.5	n.*1226A>G		non_coding_transcript_exon_variant	Exon 20 of 20	5		ENSP00000481410.1
ANTXRL	ENST00000617088.5	n.*1226A>G		3_prime_UTR_variant	Exon 20 of 20	5		ENSP00000481410.1
ANTXRL	ENST00000620264.5	c.*250A>G		downstream_gene_variant		5	NM_001278688.3	ENSP00000480615.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50891 AN: 151630 Hom.: 9600 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.345

GnomAD4 exome AF: 0.375 AC: 136426 AN: 363550 Hom.: 26282 AF XY: 0.372 AC XY: 69827 AN XY: 187936

African (AFR) AF: 0.129 AC: 1448 AN: 11262

American (AMR) AF: 0.470 AC: 6018 AN: 12792

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 4508 AN: 11744

East Asian (EAS) AF: 0.225 AC: 5651 AN: 25162

South Asian (SAS) AF: 0.281 AC: 8234 AN: 29268

European-Finnish (FIN) AF: 0.455 AC: 11419 AN: 25082

Middle Eastern (MID) AF: 0.357 AC: 597 AN: 1672

European-Non Finnish (NFE) AF: 0.403 AC: 90618 AN: 224676

Other (OTH) AF: 0.362 AC: 7933 AN: 21892

GnomAD4 genome AF: 0.335 AC: 50891 AN: 151748 Hom.: 9596 Cov.: 33 AF XY: 0.338 AC XY: 25080 AN XY: 74156

African (AFR) AF: 0.132 AC: 5487 AN: 41440

American (AMR) AF: 0.446 AC: 6800 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1387 AN: 3458

East Asian (EAS) AF: 0.238 AC: 1227 AN: 5148

South Asian (SAS) AF: 0.291 AC: 1398 AN: 4812

European-Finnish (FIN) AF: 0.457 AC: 4806 AN: 10522

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28608 AN: 67834

Other (OTH) AF: 0.340 AC: 713 AN: 2100

Alfa AF: 0.392 Hom.: 47436

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.47
PhyloP100		0.85
Mutation Taster		=97/3	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11596854; hg19: chr10-47701570;