chr7-130876506-A-G

Variant names:

• chr7-130876506-A-G
• rs34772568
• ENST00000447430.1:n.156+14304A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447430.1(LINC00513):​n.156+14304A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0952 in 152,180 control chromosomes in the GnomAD database, including 744 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 0.095 (744 hom., cov: 32)
• Consequence: LINC00513 ENST00000447430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

Genes affected

LINC00513 (HGNC:43566): (long intergenic non-protein coding RNA 513)

LINC-PINT (HGNC:26885): (long intergenic non-protein coding RNA, p53 induced transcript) Predicted to act upstream of or within several processes, including adipose tissue development; adult somatic muscle development; and hair follicle development. [provided by Alliance of Genome Resources, Apr 2022]

MIR29A (HGNC:31616): (microRNA 29a) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR29A	NR_029503.1	n.*241T>C		downstream_gene_variant
MIR29A	unassigned_transcript_1312	n.*242T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00513	ENST00000447430.1	n.156+14304A>G		intron_variant	Intron 2 of 4	5
LINC-PINT	ENST00000642963.1	n.593+7811T>C		intron_variant	Intron 5 of 6
LINC-PINT	ENST00000643866.1	n.1698-3867T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14490 AN: 152062 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0978

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

GnomAD4 genome AF: 0.0952 AC: 14495 AN: 152180 Hom.: 744 Cov.: 32 AF XY: 0.0917 AC XY: 6821 AN XY: 74410

Gnomad4 AFR AF: 0.0975

Gnomad4 AMR AF: 0.0793

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.0846

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0953 Hom.: 80

Bravo AF: 0.0957

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34772568; hg19: chr7-130561265;