5-177322927-C-G

Variant names:

• chr5-177322927-C-G
• rs10463065
• ENST00000694903.1:n.1104-5139G>C

Variant summary

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

The ENST00000694903.1(LMAN2):​n.1104-5139G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 151,808 control chromosomes in the GnomAD database, including 155 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 0.043 (155 hom., cov: 31)
• Consequence: LMAN2 ENST00000694903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

LMAN2 (HGNC:16986): (lectin, mannose binding 2) This gene encodes a type I transmembrane lectin that shuttles between the endoplasmic reticulum, the Golgi apparatus and the plasma membrane. The encoded protein binds high mannose type glycoproteins and may facilitate their sorting, trafficking and quality control. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0546 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
LMAN2	ENST00000694903.1	n.1104-5139G>C		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6469 AN: 151690 Hom.: 154 Cov.: 31

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.00751

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0427 AC: 6485 AN: 151808 Hom.: 155 Cov.: 31 AF XY: 0.0419 AC XY: 3111 AN XY: 74196

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.00751

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0413

Alfa AF: 0.0223 Hom.: 7

Bravo AF: 0.0428

Asia WGS AF: 0.0780 AC: 269 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	1.1
DANN	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10463065; hg19: chr5-176749928;