rs2458286

Positions:

• chr8-102966471-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAILR	NR_126338.1	n.518-1126C>T		intron_variant
MAILR	NR_126339.1	n.518-11116C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAILR	ENST00000517389.5	n.360-11116C>T		intron_variant		4
MAILR	ENST00000517996.5	n.605-11116C>T		intron_variant		3
MAILR	ENST00000518518.5	n.210-5850C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.597

Alfa AF: 0.642 Hom.: 64261

Bravo AF: 0.544

Asia WGS AF: 0.582 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2458286; hg19: chr8-103978699;