chr1-117373285-G-A

Position:

• chr1-117373285-G-A

Variant summary

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

The NM_006699.5(MAN1A2):​c.302+4800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,670 control chromosomes in the GnomAD database, including 44,922 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 0.77 (44922 hom., cov: 29)
• Consequence: MAN1A2 NM_006699.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAN1A2	NM_006699.5	c.302+4800G>A		intron_variant		ENST00000356554.7
MAN1A2	XM_006710302.4	c.302+4800G>A		intron_variant
MAN1A2	XM_011540536.4	c.302+4800G>A		intron_variant
MAN1A2	XM_017000115.2	c.302+4800G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAN1A2	ENST00000356554.7	c.302+4800G>A		intron_variant		1	NM_006699.5	P1
MAN1A2	ENST00000482811.1	n.543+4800G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116402 AN: 151552 Hom.: 44882 Cov.: 29

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.768 AC: 116500 AN: 151670 Hom.: 44922 Cov.: 29 AF XY: 0.766 AC XY: 56731 AN XY: 74106

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.772

Alfa AF: 0.759 Hom.: 54663

Bravo AF: 0.763

Asia WGS AF: 0.729 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs1146298; hg19: chr1-117915907;