GeneBe

rs10505040

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000517389.5(MAILR):​n.93-4410C>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
ENST00000517389.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

Publications

1 publications found
Variant links:
Genes affected
MAILR (HGNC:51558): (macrophage interferon regulatory lncRNA)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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
MAILRNR_126338.1 linkn.518-34383C>G intron_variant Intron 2 of 3
MAILRNR_126339.1 linkn.518-44373C>G intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAILRENST00000517389.5 linkn.93-4410C>G intron_variant Intron 1 of 3 4
MAILRENST00000517996.5 linkn.337+2696C>G intron_variant Intron 1 of 3 3
MAILRENST00000519181.5 linkn.111+28829C>G intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.162
AC:
24588
AN:
152048
Hom.:
2615
Cov.:
32
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.0477
AC:
1980
AN:
41548
American (AMR)
AF:
0.288
AC:
4397
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.158
AC:
547
AN:
3472
East Asian (EAS)
AF:
0.0575
AC:
298
AN:
5186
South Asian (SAS)
AF:
0.0963
AC:
464
AN:
4816
European-Finnish (FIN)
AF:
0.196
AC:
2075
AN:
10572
Middle Eastern (MID)
AF:
0.126
AC:
37
AN:
294
European-Non Finnish (NFE)
AF:
0.210
AC:
14297
AN:
67986
Other (OTH)
AF:
0.163
AC:
345
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1022
2044
3065
4087
5109
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
258
516
774
1032
1290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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
PhyloP100
0.16

Splicing

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

Publications

Other links and lift over

dbSNP: rs10505040; hg19: chr8-103945442; API