ENST00000585285.1:n.340+200A>G

Variant names:

• chr17-74748373-T-C
• rs2384952
• ENST00000585285.1:n.340+200A>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000585285.1(SLC9A3R1-AS1):​n.340+200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,918 control chromosomes in the GnomAD database, including 17,883 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17883 hom., cov: 33)
• Consequence: SLC9A3R1-AS1 ENST00000585285.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.600

Genes affected

SLC9A3R1-AS1 (HGNC:55322): (SLC9A3R1 antisense RNA 1)

MIR3615 (HGNC:38905): (microRNA 3615) 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 17-74748373-T-C is Benign according to our data. Variant chr17-74748373-T-C is described in ClinVar as [Benign]. Clinvar id is 1265446.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A3R1-AS1	NR_187307.1	n.1160+200A>G		intron_variant	Intron 2 of 2
MIR3615	NR_037409.1	n.-240T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A3R1-AS1	ENST00000585285.1	n.340+200A>G		intron_variant	Intron 1 of 1	3
MIR3615	ENST00000581999.1	n.-240T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72719 AN: 151810 Hom.: 17850 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.460

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.479 AC: 72796 AN: 151918 Hom.: 17883 Cov.: 33 AF XY: 0.481 AC XY: 35711 AN XY: 74240

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.464

Alfa AF: 0.498 Hom.: 2716

Bravo AF: 0.475

Asia WGS AF: 0.387 AC: 1335 AN: 3444

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 16, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2384952; hg19: chr17-72744512;