Genetic Variant MBL1P:n.1194A>G (chr10-79922889-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000480805.1(MBL1P):n.1194A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 154,806 control chromosomes in the GnomAD database, including 37,077 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 0.68 ( 36449 hom., cov: 31)

Exomes 𝑓: 0.67 ( 628 hom. )

Consequence

MBL1P
ENST00000480805.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.727

Publications

8 publications found

Variant links:

Genes affected

MBL1P (HGNC:):

MBL1P links:

MBL1P (HGNC:6921): (mannose binding lectin 1, pseudogene) Predicted to enable several functions, including calcium-dependent carbohydrate binding activity; mannose binding activity; and protein homodimerization activity. Predicted to be involved in protein homotrimerization. Predicted to act upstream of or within defense response to other organism and positive regulation of phagocytosis. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

MBL1P links:

BMS1P21 (HGNC:51604): (BMS1 pseudogene 21)

BMS1P21 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBL1P	NR_002724.2 link	n.1194A>G		non_coding_transcript_exon_variant	Exon 3 of 3
BMS1P21	NR_033857.1 link	n.742+901A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MBL1P	ENST00000480805.1 link	n.1194A>G	non_coding_transcript_exon_variant	Exon 3 of 3	1
MBL1P	ENST00000497731.2 link	n.615A>G	non_coding_transcript_exon_variant	Exon 4 of 4	6
ENSG00000283913	ENST00000818197.1 link	n.1248A>G	non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

103655

AN:

151874

Hom.:

36381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.850

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.650

Gnomad ASJ

AF:

0.629

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.740

Gnomad FIN

AF:

0.579

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.668

GnomAD4 exome

AF:

0.670

AC:

1885

AN:

2814

Hom.:

628

Cov.:

AF XY:

0.667

AC XY:

987

AN XY:

1480

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.643

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.713

AC:

AN:

European-Finnish (FIN)

AF:

0.562

AC:

255

AN:

454

Middle Eastern (MID)

AF:

0.694

AC:

1134

AN:

1634

European-Non Finnish (NFE)

AF:

0.615

AC:

193

AN:

314

Other (OTH)

AF:

0.748

AC:

163

AN:

218

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

118

157

196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.683

AC:

103790

AN:

151992

Hom.:

36449

Cov.:

AF XY:

0.684

AC XY:

50785

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.850

AC:

35251

AN:

41452

American (AMR)

AF:

0.651

AC:

9946

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

2185

AN:

3472

East Asian (EAS)

AF:

0.776

AC:

4002

AN:

5158

South Asian (SAS)

AF:

0.741

AC:

3559

AN:

4806

European-Finnish (FIN)

AF:

0.579

AC:

6115

AN:

10566

Middle Eastern (MID)

AF:

0.687

AC:

202

AN:

294

European-Non Finnish (NFE)

AF:

0.597

AC:

40552

AN:

67950

Other (OTH)

AF:

0.673

AC:

1421

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1621

3242

4862

6483

8104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.647

Hom.:

13239

Bravo

AF:

0.693

Asia WGS

AF:

0.777

AC:

2704

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.57

PhyloP100

0.73

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over