11-66454666-C-T

Variant names:

• chr11-66454666-C-T
• rs1791682

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0683 in 624,312 control chromosomes in the GnomAD database, including 2,396 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 0.11 (1382 hom., cov: 32)
  • Exomes 𝑓: 0.056 (1014 hom.)
• Consequence: LOC100505524 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 5 publications found

Genes affected

LOC100505524 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

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>A		intron	N/A
	ENSG00000254596	ENST00000528671.1	TSL:6	n.*85C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16052 AN: 152056 Hom.: 1381 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0966

GnomAD4 exome AF: 0.0563 AC: 26583 AN: 472138 Hom.: 1014 AF XY: 0.0558 AC XY: 12962 AN XY: 232344

African (AFR) AF: 0.251 AC: 2446 AN: 9734

American (AMR) AF: 0.0529 AC: 348 AN: 6578

Ashkenazi Jewish (ASJ) AF: 0.0693 AC: 589 AN: 8496

East Asian (EAS) AF: 0.0000734 AC: 1 AN: 13624

South Asian (SAS) AF: 0.0444 AC: 913 AN: 20568

European-Finnish (FIN) AF: 0.0572 AC: 807 AN: 14120

Middle Eastern (MID) AF: 0.102 AC: 154 AN: 1514

European-Non Finnish (NFE) AF: 0.0530 AC: 19921 AN: 375790

Other (OTH) AF: 0.0647 AC: 1404 AN: 21714

GnomAD4 genome AF: 0.106 AC: 16078 AN: 152174 Hom.: 1382 Cov.: 32 AF XY: 0.102 AC XY: 7601 AN XY: 74408

African (AFR) AF: 0.240 AC: 9948 AN: 41482

American (AMR) AF: 0.0612 AC: 935 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4820

European-Finnish (FIN) AF: 0.0486 AC: 515 AN: 10604

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0588 AC: 4002 AN: 68014

Other (OTH) AF: 0.0956 AC: 202 AN: 2114

Alfa AF: 0.0760 Hom.: 782

Bravo AF: 0.113

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs1791682; hg19: chr11-66222137;