rs7514323

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006699.5(MAN1A2):​c.951-392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 151,442 control chromosomes in the GnomAD database, including 43,289 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 0.75 ( 43289 hom., cov: 29)

Consequence

MAN1A2
NM_006699.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22
Variant links:
Genes affected
MAN1A2 (HGNC:6822): (mannosidase alpha class 1A member 2) Alpha-mannosidases function at different stages of N-glycan maturation in mammalian cells. See MAN2A1 (MIM 154582) for general information.[supplied by OMIM, Mar 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAN1A2NM_006699.5 linkuse as main transcriptc.951-392A>G intron_variant ENST00000356554.7
MAN1A2XM_006710302.4 linkuse as main transcriptc.951-392A>G intron_variant
MAN1A2XM_011540536.4 linkuse as main transcriptc.951-392A>G intron_variant
MAN1A2XM_017000115.2 linkuse as main transcriptc.950+17772A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAN1A2ENST00000356554.7 linkuse as main transcriptc.951-392A>G intron_variant 1 NM_006699.5 P1
MAN1A2ENST00000449370.6 linkuse as main transcriptc.149-392A>G intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.755
AC:
114216
AN:
151332
Hom.:
43257
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.779
Gnomad AMI
AF:
0.731
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.691
Gnomad EAS
AF:
0.603
Gnomad SAS
AF:
0.792
Gnomad FIN
AF:
0.730
Gnomad MID
AF:
0.810
Gnomad NFE
AF:
0.767
Gnomad OTH
AF:
0.766
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.755
AC:
114300
AN:
151442
Hom.:
43289
Cov.:
29
AF XY:
0.752
AC XY:
55607
AN XY:
73966
show subpopulations
Gnomad4 AFR
AF:
0.779
Gnomad4 AMR
AF:
0.703
Gnomad4 ASJ
AF:
0.691
Gnomad4 EAS
AF:
0.603
Gnomad4 SAS
AF:
0.793
Gnomad4 FIN
AF:
0.730
Gnomad4 NFE
AF:
0.767
Gnomad4 OTH
AF:
0.765
Alfa
AF:
0.766
Hom.:
6046
Bravo
AF:
0.748
Asia WGS
AF:
0.728
AC:
2528
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.072
DANN
Benign
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7514323; hg19: chr1-118002719; COSMIC: COSV62981951; API