Variant rs3835325 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_005570.4(LMAN1):c.539+11_539+12del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,430,510 control chromosomes in the GnomAD database, including 17,657 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1582 hom., cov: 30)

Exomes 𝑓: 0.15 ( 16075 hom. )

Consequence

LMAN1
NM_005570.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.412

Variant links:

Genes affected

LMAN1 (HGNC:6631): (lectin, mannose binding 1) The protein encoded by this gene is a membrane mannose-specific lectin that cycles between the endoplasmic reticulum, endoplasmic reticulum-Golgi intermediate compartment, and cis-Golgi, functioning as a cargo receptor for glycoprotein transport. The protein has an N-terminal signal sequence, a calcium-dependent and pH-sensitive carbohydrate recognition domain, a stalk region that functions in oligomerization, a transmembrane domain, and a short cytoplasmic domain required for organelle targeting. Allelic variants of this gene are associated with the autosomal recessive disorder combined factor V-factor VIII deficiency. [provided by RefSeq, Jul 2015]

LMAN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 18-59354506-AAC-A is Benign according to our data. Variant chr18-59354506-AAC-A is described in ClinVar as [Likely_benign]. Clinvar id is 259797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMAN1	NM_005570.4 linkuse as main transcript	c.539+11_539+12del		intron_variant		ENST00000251047.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMAN1	ENST00000251047.6 linkuse as main transcript	c.539+11_539+12del		intron_variant		1	NM_005570.4	P1
LMAN1	ENST00000587561.1 linkuse as main transcript	n.560+11_560+12del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20717

AN:

152030

Hom.:

1577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0614

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.0288

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.129

GnomAD3 exomes

AF:

0.150

AC:

37392

AN:

249170

Hom.:

3044

AF XY:

0.153

AC XY:

20577

AN XY:

134712

show subpopulations

Gnomad AFR exome

AF:

0.0560

Gnomad AMR exome

AF:

0.165

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.0272

Gnomad SAS exome

AF:

0.150

Gnomad FIN exome

AF:

0.162

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.153

AC:

195436

AN:

1278364

Hom.:

16075

AF XY:

0.154

AC XY:

99568

AN XY:

645594

show subpopulations

Gnomad4 AFR exome

AF:

0.0510

Gnomad4 AMR exome

AF:

0.166

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.0194

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.136

AC:

20723

AN:

152146

Hom.:

1582

Cov.:

AF XY:

0.136

AC XY:

10087

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0612

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.0287

Gnomad4 SAS

AF:

0.145

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.177

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.155

Hom.:

359

Bravo

AF:

0.132

Asia WGS

AF:

0.0860

AC:

297

AN:

3464

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Factor V and factor VIII, combined deficiency of, type 1

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over