dbSNP rs7976497: MLEC:c.*1119T>C (chr12-120697664-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_014730.4(MLEC):c.*1119T>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 0.595 in 152,578 control chromosomes in the GnomAD database, including 29,774 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 0.60 ( 29734 hom., cov: 33)

Exomes 𝑓: 0.46 ( 40 hom. )

Consequence

MLEC
NM_014730.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

22 publications found

Variant links:

Genes affected

MLEC (HGNC:28973): (malectin) This gene encodes the carbohydrate-binding protein malectin which is a Type I membrane-anchored endoplasmic reticulum protein. This protein has an affinity for Glc2Man9GlcNAc2 (G2M9) N-glycans and is involved in regulating glycosylation in the endoplasmic reticulum. This protein has also been shown to interact with ribophorin I and may be involved in the directing the degradation of misfolded proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

MLEC links:

ENSG00000256364 (HGNC:):

ENSG00000256364 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014730.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MLEC	NM_014730.4	MANE Select	c.*1119T>C	3_prime_UTR	Exon 5 of 5	NP_055545.1
MLEC	NM_001303628.2		c.*1109T>C	3_prime_UTR	Exon 3 of 3	NP_001290557.1
MLEC	NM_001303627.2		c.*1119T>C	3_prime_UTR	Exon 5 of 5	NP_001290556.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MLEC	ENST00000228506.8	TSL:1 MANE Select	c.*1119T>C	3_prime_UTR	Exon 5 of 5	ENSP00000228506.3
MLEC	ENST00000545525.6	TSL:2	c.*1119T>C	3_prime_UTR	Exon 4 of 4	ENSP00000438950.2
MLEC	ENST00000535413.1	TSL:2	n.139+1123T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.595

AC:

90507

AN:

152026

Hom.:

29679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.884

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.596

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.646

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.586

GnomAD4 exome

AF:

0.459

AC:

199

AN:

434

Hom.:

Cov.:

AF XY:

0.492

AC XY:

126

AN XY:

256

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.457

AC:

189

AN:

414

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.524

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.596

AC:

90615

AN:

152144

Hom.:

29734

Cov.:

AF XY:

0.601

AC XY:

44709

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.884

AC:

36748

AN:

41552

American (AMR)

AF:

0.595

AC:

9100

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.509

AC:

1766

AN:

3468

East Asian (EAS)

AF:

0.532

AC:

2754

AN:

5172

South Asian (SAS)

AF:

0.646

AC:

3116

AN:

4824

European-Finnish (FIN)

AF:

0.462

AC:

4880

AN:

10562

Middle Eastern (MID)

AF:

0.612

AC:

180

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30424

AN:

67958

Other (OTH)

AF:

0.589

AC:

1247

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1666

3332

4997

6663

8329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

728

1456

2184

2912

3640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.501

Hom.:

83316

Bravo

AF:

0.617

Asia WGS

AF:

0.629

AC:

2185

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over