rs10917413

Variant names:

• chr1-23691787-C-G
• rs10917413
• ENST00000374550.8:c.-37C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-23691787-C-G
• chr1-23691787-C-A
• chr1-23691787-C-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001199802.1(RPL11):​c.-37C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.997 in 1,614,208 control chromosomes in the GnomAD database, including 802,105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.98 (73853 hom., cov: 34)
  • Exomes 𝑓: 1.0 (728252 hom.)
• Consequence: RPL11 NM_001199802.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.73
• Publications: 12 publications found

Genes affected

RPL11 (HGNC:10301): (ribosomal protein L11) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L5P family of ribosomal proteins. It is located in the cytoplasm. The protein probably associates with the 5S rRNA. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Dec 2010]

RPL11 Gene-Disease associations (from GenCC):

• Diamond-Blackfan anemia 7

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia
• Diamond-Blackfan anemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 1-23691787-C-G is Benign according to our data. Variant chr1-23691787-C-G is described in ClinVar as Benign. ClinVar VariationId is 138926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199802.1. 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
	RPL11	NM_001199802.1		c.-37C>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 6	NP_001186731.1	P62913-2
	RPL11	NM_001199802.1		c.-37C>G		5_prime_UTR	Exon 1 of 6	NP_001186731.1	P62913-2
	RPL11	NM_000975.5	MANE Select	c.-37C>G		upstream_gene	N/A	NP_000966.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL11	ENST00000374550.8	TSL:1	c.-37C>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 6	ENSP00000363676.4	P62913-2
	RPL11	ENST00000374550.8	TSL:1	c.-37C>G		5_prime_UTR	Exon 1 of 6	ENSP00000363676.4	P62913-2
	RPL11	ENST00000933792.1		c.-37C>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 6	ENSP00000603851.1

Frequencies

GnomAD3 genomes AF: 0.984 AC: 149870 AN: 152258 Hom.: 73800 Cov.: 34

Gnomad AFR AF: 0.947

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.987

GnomAD2 exomes AF: 0.995 AC: 250292 AN: 251444 AF XY: 0.996

Gnomad AFR exome AF: 0.947

Gnomad AMR exome AF: 0.997

Gnomad ASJ exome AF: 1.00

Gnomad EAS exome AF: 0.998

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 1.00

Gnomad OTH exome AF: 0.997

GnomAD4 exome AF: 0.998 AC: 1459114 AN: 1461832 Hom.: 728252 Cov.: 44 AF XY: 0.998 AC XY: 725983 AN XY: 727218

African (AFR) AF: 0.947 AC: 31697 AN: 33470

American (AMR) AF: 0.996 AC: 44541 AN: 44722

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 26136 AN: 26136

East Asian (EAS) AF: 0.999 AC: 39655 AN: 39694

South Asian (SAS) AF: 0.997 AC: 86014 AN: 86258

European-Finnish (FIN) AF: 1.00 AC: 53405 AN: 53416

Middle Eastern (MID) AF: 0.995 AC: 5738 AN: 5768

European-Non Finnish (NFE) AF: 1.00 AC: 1111810 AN: 1111972

Other (OTH) AF: 0.995 AC: 60118 AN: 60396

GnomAD4 genome AF: 0.984 AC: 149981 AN: 152376 Hom.: 73853 Cov.: 34 AF XY: 0.984 AC XY: 73357 AN XY: 74518

African (AFR) AF: 0.947 AC: 39374 AN: 41576

American (AMR) AF: 0.992 AC: 15188 AN: 15312

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5179 AN: 5188

South Asian (SAS) AF: 0.998 AC: 4820 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68028 AN: 68046

Other (OTH) AF: 0.987 AC: 2089 AN: 2116

Alfa AF: 0.997 Hom.: 8014

Bravo AF: 0.982

Asia WGS AF: 0.992 AC: 3451 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Diamond-Blackfan anemia (1)
-	-	1	Diamond-Blackfan anemia 7 (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		1.7
PromoterAI		0.057	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10917413; hg19: chr1-24018277;