chr6-69804858-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000647964.1(LMBRD1):​c.-150-14386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,012 control chromosomes in the GnomAD database, including 14,938 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 0.44 ( 14938 hom., cov: 32)

Consequence

LMBRD1
ENST00000647964.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.456
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LMBRD1ENST00000647964.1 linkc.-150-14386G>A intron_variant Intron 2 of 16 ENSP00000496784.1 Q9NUN5-3
LMBRD1ENST00000648394.1 linkc.-150-14386G>A intron_variant Intron 1 of 15 ENSP00000497302.1 Q9NUN5-3
LMBRD1ENST00000649028.1 linkc.-150-14386G>A intron_variant Intron 2 of 16 ENSP00000498034.1 Q9NUN5-3

Frequencies

GnomAD3 genomes
AF:
0.440
AC:
66765
AN:
151894
Hom.:
14929
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.511
Gnomad AMI
AF:
0.398
Gnomad AMR
AF:
0.427
Gnomad ASJ
AF:
0.432
Gnomad EAS
AF:
0.547
Gnomad SAS
AF:
0.445
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.407
Gnomad OTH
AF:
0.438
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.439
AC:
66800
AN:
152012
Hom.:
14938
Cov.:
32
AF XY:
0.435
AC XY:
32352
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.510
Gnomad4 AMR
AF:
0.427
Gnomad4 ASJ
AF:
0.432
Gnomad4 EAS
AF:
0.547
Gnomad4 SAS
AF:
0.445
Gnomad4 FIN
AF:
0.338
Gnomad4 NFE
AF:
0.407
Gnomad4 OTH
AF:
0.436
Alfa
AF:
0.414
Hom.:
13144
Bravo
AF:
0.446
Asia WGS
AF:
0.488
AC:
1699
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.6
DANN
Benign
0.34

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: rs9364063; hg19: chr6-70514750; COSMIC: COSV69404036; API