6-69675763-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018368.4(LMBRD1):​c.*395T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00825 in 209,490 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0070 ( 22 hom., cov: 32)
Exomes 𝑓: 0.012 ( 18 hom. )

Consequence

LMBRD1
NM_018368.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0840
Variant links:
Genes affected
LMBRD1 (HGNC:23038): (LMBR1 domain containing 1) This gene encodes a lysosomal membrane protein that may be involved in the transport and metabolism of cobalamin. This protein also interacts with the large form of the hepatitis delta antigen and may be required for the nucleocytoplasmic shuttling of the hepatitis delta virus. Mutations in this gene are associated with the vitamin B12 metabolism disorder termed, homocystinuria-megaloblastic anemia complementation type F.[provided by RefSeq, Oct 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 6-69675763-A-G is Benign according to our data. Variant chr6-69675763-A-G is described in ClinVar as [Benign]. Clinvar id is 357764.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LMBRD1NM_018368.4 linkuse as main transcriptc.*395T>C 3_prime_UTR_variant 16/16 ENST00000649934.3 NP_060838.3
LMBRD1NM_001363722.2 linkuse as main transcriptc.*395T>C 3_prime_UTR_variant 16/16 NP_001350651.1
LMBRD1NM_001367271.1 linkuse as main transcriptc.*395T>C 3_prime_UTR_variant 16/16 NP_001354200.1
LMBRD1NM_001367272.1 linkuse as main transcriptc.*395T>C 3_prime_UTR_variant 16/16 NP_001354201.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LMBRD1ENST00000649934.3 linkuse as main transcriptc.*395T>C 3_prime_UTR_variant 16/16 NM_018368.4 ENSP00000497690 P2Q9NUN5-1
LMBRD1ENST00000651675.1 linkuse as main transcriptc.*18+377T>C intron_variant ENSP00000498850
LMBRD1ENST00000647655.1 linkuse as main transcript downstream_gene_variant
LMBRD1ENST00000648265.1 linkuse as main transcript downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.00703
AC:
1070
AN:
152180
Hom.:
22
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00101
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0785
Gnomad SAS
AF:
0.0184
Gnomad FIN
AF:
0.0301
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00290
Gnomad OTH
AF:
0.00191
GnomAD4 exome
AF:
0.0115
AC:
660
AN:
57192
Hom.:
18
Cov.:
0
AF XY:
0.0123
AC XY:
376
AN XY:
30450
show subpopulations
Gnomad4 AFR exome
AF:
0.000929
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0715
Gnomad4 SAS exome
AF:
0.0202
Gnomad4 FIN exome
AF:
0.0281
Gnomad4 NFE exome
AF:
0.00494
Gnomad4 OTH exome
AF:
0.0131
GnomAD4 genome
AF:
0.00702
AC:
1069
AN:
152298
Hom.:
22
Cov.:
32
AF XY:
0.00913
AC XY:
680
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.00101
Gnomad4 AMR
AF:
0.000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0785
Gnomad4 SAS
AF:
0.0184
Gnomad4 FIN
AF:
0.0301
Gnomad4 NFE
AF:
0.00290
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00526
Hom.:
1
Bravo
AF:
0.00419
Asia WGS
AF:
0.0380
AC:
132
AN:
3470

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Methylmalonic aciduria and homocystinuria type cblF Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.6
DANN
Benign
0.54

Splicing

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: rs80330045; hg19: chr6-70385655; API