Variant 14-100883961-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001134888.3(RTL1):c.828A>G(p.Glu276Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 1,551,280 control chromosomes in the GnomAD database, including 283,868 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27373 hom., cov: 32)

Exomes 𝑓: 0.60 ( 256495 hom. )

Consequence

RTL1
NM_001134888.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.81

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:

RTL1 (HGNC:):

RTL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 14-100883961-T-C is Benign according to our data. Variant chr14-100883961-T-C is described in ClinVar as [Benign]. Clinvar id is 1334333.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.81 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RTL1	NM_001134888.3 linkuse as main transcript	c.828A>G	p.Glu276Glu	synonymous_variant	4/4	ENST00000649591.1	NP_001128360.1	A6NKG5B9EK54
RTL1	XM_047431358.1 linkuse as main transcript	c.828A>G	p.Glu276Glu	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RTL1	ENST00000649591.1 linkuse as main transcript	c.828A>G	p.Glu276Glu	synonymous_variant	4/4		NM_001134888.3	ENSP00000497482.1	A6NKG5
MIR493HG	ENST00000699458.1 linkuse as main transcript	n.905T>C		non_coding_transcript_exon_variant	1/6
MIR493HG	ENST00000637474.1 linkuse as main transcript	n.109-5688T>C		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.594

AC:

90211

AN:

151848

Hom.:

27363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.583

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.703

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.603

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.630

Gnomad OTH

AF:

0.620

GnomAD3 exomes

AF:

0.534

AC:

82194

AN:

153990

Hom.:

23459

AF XY:

0.534

AC XY:

43625

AN XY:

81706

show subpopulations

Gnomad AFR exome

AF:

0.623

Gnomad AMR exome

AF:

0.337

Gnomad ASJ exome

AF:

0.700

Gnomad EAS exome

AF:

0.410

Gnomad SAS exome

AF:

0.398

Gnomad FIN exome

AF:

0.605

Gnomad NFE exome

AF:

0.633

Gnomad OTH exome

AF:

0.580

GnomAD4 exome

AF:

0.600

AC:

839811

AN:

1399314

Hom.:

256495

Cov.:

AF XY:

0.595

AC XY:

410957

AN XY:

690160

show subpopulations

Gnomad4 AFR exome

AF:

0.618

Gnomad4 AMR exome

AF:

0.355

Gnomad4 ASJ exome

AF:

0.701

Gnomad4 EAS exome

AF:

0.420

Gnomad4 SAS exome

AF:

0.402

Gnomad4 FIN exome

AF:

0.604

Gnomad4 NFE exome

AF:

0.626

Gnomad4 OTH exome

AF:

0.600

GnomAD4 genome

AF:

0.594

AC:

90255

AN:

151966

Hom.:

27373

Cov.:

AF XY:

0.585

AC XY:

43454

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.616

Gnomad4 AMR

AF:

0.454

Gnomad4 ASJ

AF:

0.703

Gnomad4 EAS

AF:

0.414

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.603

Gnomad4 NFE

AF:

0.630

Gnomad4 OTH

AF:

0.615

Alfa

AF:

0.619

Hom.:

78226

Bravo

AF:

0.583

Asia WGS

AF:

0.417

AC:

1448

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 14, 2022	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.046

DANN

Benign

0.65

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over