chr6-119179509-G-A

Position:

• chr6-119179509-G-A

Variant summary

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

The NM_005907.4(MAN1A1):​c.*310C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 168,098 control chromosomes in the GnomAD database, including 13,645 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 0.40 (12307 hom., cov: 32)
  • Exomes 𝑓: 0.39 (1338 hom.)
• Consequence: MAN1A1 NM_005907.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05

Genes affected

MAN1A1 (HGNC:6821): (mannosidase alpha class 1A member 1) This gene encodes a class I mammalian Golgi 1,2-mannosidase which is a type II transmembrane protein. This protein catalyzes the hydrolysis of three terminal mannose residues from peptide-bound Man(9)-GlcNAc(2) oligosaccharides and belongs to family 47 of glycosyl hydrolases. [provided by RefSeq, Jul 2012]

ENSG00000253194 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAN1A1	NM_005907.4	c.*310C>T		3_prime_UTR_variant	13/13	ENST00000368468.4	NP_005898.2
MAN1A1	XM_005266986.5	c.*310C>T		3_prime_UTR_variant	13/13		XP_005267043.1
MAN1A1	XM_011535833.3	c.*310C>T		3_prime_UTR_variant	12/12		XP_011534135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAN1A1	ENST00000368468	c.*310C>T		3_prime_UTR_variant	13/13	2	NM_005907.4	ENSP00000357453.3
ENSG00000253194	ENST00000518570.2	n.457-348G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60394 AN: 151850 Hom.: 12294 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.388 AC: 6256 AN: 16130 Hom.: 1338 Cov.: 0 AF XY: 0.387 AC XY: 3306 AN XY: 8552

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.346

Gnomad4 ASJ exome AF: 0.373

Gnomad4 EAS exome AF: 0.374

Gnomad4 SAS exome AF: 0.491

Gnomad4 FIN exome AF: 0.458

Gnomad4 NFE exome AF: 0.382

Gnomad4 OTH exome AF: 0.413

GnomAD4 genome AF: 0.398 AC: 60453 AN: 151968 Hom.: 12307 Cov.: 32 AF XY: 0.401 AC XY: 29794 AN XY: 74242

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.391

Alfa AF: 0.402 Hom.: 11989

Bravo AF: 0.387

Asia WGS AF: 0.461 AC: 1604 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	7.7
DANN	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs2558; hg19: chr6-119500674;