ENST00000517389.5:n.360-13826A>G

Variant names:

• chr8-102963761-A-G
• rs6468852
• ENST00000517389.5:n.360-13826A>G

Variant summary

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

The ENST00000517389.5(MAILR):​n.360-13826A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,130 control chromosomes in the GnomAD database, including 9,880 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 0.29 (9880 hom., cov: 32)
• Consequence: MAILR ENST00000517389.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 7 publications found

Genes affected

MAILR (HGNC:51558): (macrophage interferon regulatory lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517389.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAILR	NR_126338.1		n.518-3836A>G		intron	N/A
	MAILR	NR_126339.1		n.518-13826A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAILR	ENST00000517389.5	TSL:4	n.360-13826A>G		intron	N/A
	MAILR	ENST00000517996.5	TSL:3	n.605-13826A>G		intron	N/A
	MAILR	ENST00000518518.5	TSL:5	n.210-8560A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44149 AN: 152012 Hom.: 9843 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.291 AC: 44235 AN: 152130 Hom.: 9880 Cov.: 32 AF XY: 0.283 AC XY: 21084 AN XY: 74380

African (AFR) AF: 0.631 AC: 26157 AN: 41474

American (AMR) AF: 0.182 AC: 2783 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3468

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5178

South Asian (SAS) AF: 0.176 AC: 849 AN: 4822

European-Finnish (FIN) AF: 0.139 AC: 1470 AN: 10582

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11107 AN: 68004

Other (OTH) AF: 0.262 AC: 553 AN: 2114

Alfa AF: 0.219 Hom.: 10485

Bravo AF: 0.310

Asia WGS AF: 0.139 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.72
DANN	Benign	0.72
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs6468852; hg19: chr8-103975989;