rs7176022

Positions:

• chr15-74815539-A-C
• chr15-74815539-A-G
• chr15-74815539-A-T

Variant summary

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

The NM_021819.3(LMAN1L):​c.176-618A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,084 control chromosomes in the GnomAD database, including 33,249 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 0.66 (33249 hom., cov: 33)
• Consequence: LMAN1L NM_021819.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

LMAN1L (HGNC:6632): (lectin, mannose binding 1 like) This gene encodes a mannose-binding type 1 transmembrane protein that contains an N-terminal lectin-like carbohydrate recognition domain. The encoded protein is similar in structure to lectins found in leguminous plants. This lectin is thought to transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMAN1L	NM_021819.3	c.176-618A>C		intron_variant		ENST00000309664.10	NP_068591.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMAN1L	ENST00000309664.10	c.176-618A>C		intron_variant		1	NM_021819.3	ENSP00000310431	P1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99908 AN: 151966 Hom.: 33241 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.657 AC: 99962 AN: 152084 Hom.: 33249 Cov.: 33 AF XY: 0.651 AC XY: 48425 AN XY: 74340

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.639

Alfa AF: 0.608 Hom.: 3701

Bravo AF: 0.646

Asia WGS AF: 0.672 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.46

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: rs7176022; hg19: chr15-75107880;