rs10505040

Variant names:

• chr8-102933214-C-G
• rs10505040
• ENST00000517389.5:n.93-4410C>G

Variant summary

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

The ENST00000517996.5(MAILR):​n.337+2696C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,166 control chromosomes in the GnomAD database, including 2,615 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 0.16 (2615 hom., cov: 32)
• Consequence: MAILR ENST00000517996.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAILR	NR_126338.1	n.518-34383C>G		intron_variant	Intron 2 of 3
MAILR	NR_126339.1	n.518-44373C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAILR	ENST00000517389.5	n.93-4410C>G		intron_variant	Intron 1 of 3	4
MAILR	ENST00000517996.5	n.337+2696C>G		intron_variant	Intron 1 of 3	3
MAILR	ENST00000519181.5	n.111+28829C>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24588 AN: 152048 Hom.: 2615 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0573

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.162 AC: 24595 AN: 152166 Hom.: 2615 Cov.: 32 AF XY: 0.162 AC XY: 12015 AN XY: 74372

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0575

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.163

Alfa AF: 0.186 Hom.: 383

Bravo AF: 0.163

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505040; hg19: chr8-103945442;