rs76090066

Positions:

• chr14-100881018-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_001134888.3(RTL1):​c.3771G>A​(p.Gln1257=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,590,188 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0011 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0017 (3 hom.)
• Consequence: RTL1 NM_001134888.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.21

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]

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BP6: Variant 14-100881018-C-T is Benign according to our data. Variant chr14-100881018-C-T is described in ClinVar as [Benign]. Clinvar id is 711467.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr14-100881018-C-T is described in Lovd as [Likely_benign].
• BP7: Synonymous conserved (PhyloP=3.21 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RTL1	NM_001134888.3	c.3771G>A	p.Gln1257=	synonymous_variant	4/4	ENST00000649591.1
MIR431	NR_029965.1	n.12C>T		non_coding_transcript_exon_variant	1/1
RTL1	XM_047431358.1	c.3771G>A	p.Gln1257=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RTL1	ENST00000649591.1	c.3771G>A	p.Gln1257=	synonymous_variant	4/4		NM_001134888.3	P1
MIR431	ENST00000385266.1	n.12C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.00111 AC: 169 AN: 152186 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000289

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00221

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00101 AC: 216 AN: 213250 Hom.: 1 AF XY: 0.000893 AC XY: 103 AN XY: 115356

Gnomad AFR exome AF: 0.000540

Gnomad AMR exome AF: 0.000159

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000378

Gnomad FIN exome AF: 0.000426

Gnomad NFE exome AF: 0.00192

Gnomad OTH exome AF: 0.00146

GnomAD4 exome AF: 0.00170 AC: 2440 AN: 1437884 Hom.: 3 Cov.: 88 AF XY: 0.00168 AC XY: 1195 AN XY: 713116

Gnomad4 AFR exome AF: 0.000303

Gnomad4 AMR exome AF: 0.000143

Gnomad4 ASJ exome AF: 0.0000389

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000364

Gnomad4 FIN exome AF: 0.000571

Gnomad4 NFE exome AF: 0.00208

Gnomad4 OTH exome AF: 0.00121

GnomAD4 genome AF: 0.00111 AC: 169 AN: 152304 Hom.: 0 Cov.: 33 AF XY: 0.00106 AC XY: 79 AN XY: 74476

Gnomad4 AFR AF: 0.000289

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00221

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00181 Hom.: 0

Bravo AF: 0.00102

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	21
DANN	Benign	0.95

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

Other links and lift over

dbSNP: rs76090066; hg19: chr14-101347355;