rs1358379

Variant names:

• chr6-71403739-T-C
• rs1358379
• ENST00000413945.6:n.344+12671A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413945.6(LINC00472):​n.344+12671A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 350,218 control chromosomes in the GnomAD database, including 559 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.060 (319 hom., cov: 32)
  • Exomes 𝑓: 0.040 (240 hom.)
• Consequence: LINC00472 ENST00000413945.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 10 publications found

Genes affected

LINC00472 (HGNC:21380): (long intergenic non-protein coding RNA 472)

MIR30A (HGNC:31624): (microRNA 30a) 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 encoded miRNA is one of five members of the miR-30 family of highly conserved miRNAs and participates in many cellular processes. It has additionally been implicated in the development of several types of cancer. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2017]

ENSG00000294688 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR30A	NR_029504.1	n.-118A>G		upstream_gene_variant
MIR30A	unassigned_transcript_1150	n.-164A>G		upstream_gene_variant
MIR30A	unassigned_transcript_1151	n.-123A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00472	ENST00000413945.6	n.344+12671A>G		intron_variant	Intron 3 of 3	3
LINC00472	ENST00000436803.6	n.479+12671A>G		intron_variant	Intron 3 of 3	5
LINC00472	ENST00000602823.1	n.267+12671A>G		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9074 AN: 152128 Hom.: 318 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.0540

GnomAD4 exome AF: 0.0404 AC: 7991 AN: 197972 Hom.: 240 AF XY: 0.0381 AC XY: 4144 AN XY: 108902

African (AFR) AF: 0.0926 AC: 459 AN: 4958

American (AMR) AF: 0.0218 AC: 212 AN: 9704

Ashkenazi Jewish (ASJ) AF: 0.0368 AC: 174 AN: 4726

East Asian (EAS) AF: 0.000274 AC: 2 AN: 7294

South Asian (SAS) AF: 0.0238 AC: 949 AN: 39892

European-Finnish (FIN) AF: 0.0489 AC: 881 AN: 18028

Middle Eastern (MID) AF: 0.0326 AC: 75 AN: 2300

European-Non Finnish (NFE) AF: 0.0475 AC: 4847 AN: 102044

Other (OTH) AF: 0.0434 AC: 392 AN: 9026

GnomAD4 genome AF: 0.0597 AC: 9083 AN: 152246 Hom.: 319 Cov.: 32 AF XY: 0.0585 AC XY: 4352 AN XY: 74442

African (AFR) AF: 0.101 AC: 4211 AN: 41526

American (AMR) AF: 0.0307 AC: 469 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4826

European-Finnish (FIN) AF: 0.0488 AC: 518 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0508 AC: 3453 AN: 68028

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0569 Hom.: 30

Bravo AF: 0.0602

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1358379; hg19: chr6-72113442;