Genetic Variant MAN1A2:c.856-77A>G (chr1-117442154-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006699.5(MAN1A2):c.856-77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000131 in 762,780 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000013 ( 0 hom. )

Consequence

MAN1A2
NM_006699.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.416

Publications

5 publications found

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]

MAN1A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MAN1A2	NM_006699.5 link	c.856-77A>G	intron_variant	Intron 5 of 12	ENST00000356554.7	NP_006690.1	O60476
MAN1A2	XM_006710302.4 link	c.856-77A>G	intron_variant	Intron 5 of 13		XP_006710365.1
MAN1A2	XM_011540536.4 link	c.856-77A>G	intron_variant	Intron 5 of 12		XP_011538838.1
MAN1A2	XM_017000115.2 link	c.856-77A>G	intron_variant	Intron 5 of 6		XP_016855604.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAN1A2	ENST00000356554.7 link	c.856-77A>G		intron_variant	Intron 5 of 12	1	NM_006699.5	ENSP00000348959.3		O60476
MAN1A2	ENST00000449370.6 link	c.52-77A>G		intron_variant	Intron 1 of 8	2		ENSP00000412706.2		H0Y7H1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000131

AC:

AN:

762780

Hom.:

AF XY:

0.00

AC XY:

AN XY:

405294

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

19880

American (AMR)

AF:

0.00

AC:

AN:

42422

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20928

East Asian (EAS)

AF:

0.00

AC:

AN:

35976

South Asian (SAS)

AF:

0.00

AC:

AN:

69300

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49964

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4110

European-Non Finnish (NFE)

AF:

0.00000207

AC:

AN:

483158

Other (OTH)

AF:

0.00

AC:

AN:

37042

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.9

(source)

DANN

Benign

0.54

PhyloP100

0.42

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over