rs1054053

Variant names:

• chr10-79922889-A-C
• rs1054053
• ENST00000480805.1:n.1194A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-79922889-A-C
• chr10-79922889-A-G
• chr10-79922889-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000480805.1(MBL1P):​n.1194A>C 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)
• Consequence: MBL1P ENST00000480805.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727
• Publications: 8 publications found

Genes affected

MBL1P (HGNC:):

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]

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

ACMG classification

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=-0.56).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBL1P	ENST00000480805.1	n.1194A>C		non_coding_transcript_exon_variant	Exon 3 of 3	1
MBL1P	ENST00000497731.2	n.615A>C		non_coding_transcript_exon_variant	Exon 4 of 4	6
ENSG00000283913	ENST00000818197.1	n.1248A>C		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.56
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs1054053; hg19: chr10-81682645;