rs2458286

Variant names:

• chr8-102966471-C-T
• rs2458286
• ENST00000517389.5:n.360-11116C>T

Variant summary

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

The ENST00000519648.1(MAILR):​n.210-11116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,998 control chromosomes in the GnomAD database, including 26,052 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 0.56 (26052 hom., cov: 31)
• Consequence: MAILR ENST00000519648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAILR	NR_126338.1		n.518-1126C>T		intron	N/A
	MAILR	NR_126339.1		n.518-11116C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAILR	ENST00000517389.5	TSL:4	n.360-11116C>T		intron	N/A
	MAILR	ENST00000517996.5	TSL:3	n.605-11116C>T		intron	N/A
	MAILR	ENST00000518518.5	TSL:5	n.210-5850C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85054 AN: 151880 Hom.: 26042 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.560 AC: 85089 AN: 151998 Hom.: 26052 Cov.: 31 AF XY: 0.567 AC XY: 42129 AN XY: 74274

African (AFR) AF: 0.293 AC: 12149 AN: 41438

American (AMR) AF: 0.684 AC: 10459 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3130 AN: 5166

South Asian (SAS) AF: 0.607 AC: 2924 AN: 4814

European-Finnish (FIN) AF: 0.719 AC: 7591 AN: 10552

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44701 AN: 67962

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.626 Hom.: 133876

Bravo AF: 0.544

Asia WGS AF: 0.582 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2458286; hg19: chr8-103978699;