dbSNP rs780698489: RTL1:p.Arg1281Leu (chr14-100880947-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001134888.3(RTL1):c.3842G>T(p.Arg1281Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1281H) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.000012 ( 0 hom. )

Consequence

RTL1
NM_001134888.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.675

Publications

0 publications found

Variant links:

Genes affected

RTL1 (HGNC:14665): (retrotransposon Gag like 1) This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009]

RTL1 links:

MIR493HG (HGNC:55978): (MIR493 cluster host gene)

MIR493HG links:

MIR431 (HGNC:32027): (microRNA 431) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR431 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.09175956).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134888.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RTL1	NM_001134888.3	MANE Select	c.3842G>T	p.Arg1281Leu	missense	Exon 4 of 4	NP_001128360.1	A6NKG5
RTL1	NM_001425285.1		c.3842G>T	p.Arg1281Leu	missense	Exon 3 of 3	NP_001412214.1	A6NKG5
MIR431	NR_029965.1		n.-60C>A		upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RTL1	ENST00000649591.1	MANE Select	c.3842G>T	p.Arg1281Leu	missense	Exon 4 of 4	ENSP00000497482.1	A6NKG5
MIR493HG	ENST00000637474.1	TSL:5	n.109-8702C>A		intron	N/A
MIR431	ENST00000385266.1	TSL:6	n.-60C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000123

AC:

AN:

81234

Hom.:

Cov.:

AF XY:

0.0000225

AC XY:

AN XY:

44406

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

1242

American (AMR)

AF:

0.00

AC:

AN:

3658

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3876

East Asian (EAS)

AF:

0.00

AC:

AN:

428

South Asian (SAS)

AF:

0.0000822

AC:

AN:

12162

European-Finnish (FIN)

AF:

0.00

AC:

AN:

15700

Middle Eastern (MID)

AF:

0.00

AC:

AN:

806

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

40768

Other (OTH)

AF:

0.00

AC:

AN:

2594

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

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.080

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.94

FATHMM_MKL

Benign

0.047

LIST_S2

Benign

0.47

M_CAP

Benign

0.047

MetaRNN

Benign

0.092

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

PhyloP100

-0.68

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.50

REVEL

Benign

0.041

Sift

Uncertain

0.0070

Sift4G

Pathogenic

0.0

Vest4

0.19

MutPred

0.40

Gain of catalytic residue at R1281 (P = 2e-04)

MVP

0.17

MPC

0.78

ClinPred

0.23

GERP RS

-0.65

Varity_R

0.068

gMVP

0.12

Mutation Taster

=99/1

polymorphism

(source)

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

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