dbSNP rs1791682: LOC100505524:n.66454666C>A (chr11-66454666-C-A) – 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 variant allele was found at a frequency of 0.00000212 in 472,716 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

LOC100505524
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.911

Publications

5 publications found

Variant links:

Genes affected

LOC100505524 (HGNC:):

LOC100505524 links:

MRPL11 (HGNC:14042): (mitochondrial ribosomal protein L11) This nuclear gene encodes a 39S subunit component of the mitochondial ribosome. Alternative splicing results in multiple transcript variants. Pseudogenes for this gene are found on chromosomes 5 and 12. [provided by RefSeq, May 2014]

MRPL11 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=-0.59).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524576.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL11	ENST00000524576.5	TSL:2	n.826+11247G>T		intron	N/A
	ENSG00000254596	ENST00000528671.1	TSL:6	n.*85C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000212

AC:

AN:

472716

Hom.:

AF XY:

0.00

AC XY:

AN XY:

232634

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

9754

American (AMR)

AF:

0.00

AC:

AN:

6580

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8508

East Asian (EAS)

AF:

0.00

AC:

AN:

13624

South Asian (SAS)

AF:

0.00

AC:

AN:

20584

European-Finnish (FIN)

AF:

0.00

AC:

AN:

14130

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1514

European-Non Finnish (NFE)

AF:

0.00000266

AC:

AN:

376278

Other (OTH)

AF:

0.00

AC:

AN:

21744

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.91

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