Genetic Variant MBL1P:n.1194A>T (chr10-79922889-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000480805.1(MBL1P):n.1194A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000480805.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBL1P	NR_002724.2		n.1194A>T		non_coding_transcript_exon	Exon 3 of 3
	BMS1P21	NR_033857.1		n.742+901A>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MBL1P	ENST00000480805.1	TSL:1	n.1194A>T	non_coding_transcript_exon	Exon 3 of 3
MBL1P	ENST00000497731.2	TSL:6	n.615A>T	non_coding_transcript_exon	Exon 4 of 4
ENSG00000283913	ENST00000818197.1		n.1248A>T	non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

2816

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

1482

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

454

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1634

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

316

Other (OTH)

AF:

0.00

AC:

AN:

218

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.68

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over