16-70030358-C-T

Position:

• chr16-70030358-C-T

Variant summary

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

The NR_036265.1(MIR1972-2):​n.13C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 154,316 control chromosomes in the GnomAD database, including 2,378 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 0.15 (2342 hom., cov: 32)
  • Exomes 𝑓: 0.14 (36 hom.)
• Consequence: MIR1972-2 NR_036265.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

MIR1972-2 (HGNC:38252): (microRNA 1972-2) 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]

PDXDC2P (HGNC:27559): (pyridoxal dependent decarboxylase domain containing 2, pseudogene) Predicted to enable carboxy-lyase activity and pyridoxal phosphate binding activity. Predicted to be involved in carboxylic acid metabolic process. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

PDXDC2P-NPIPB14P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR1972-2	NR_036265.1	n.13C>T		non_coding_transcript_exon_variant	1/1
PDXDC2P-NPIPB14P	NR_003610.1	n.899+630G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1972-2	ENST00000458813.1	n.13C>T		non_coding_transcript_exon_variant	1/1
PDXDC2P	ENST00000534700.6	n.727+630G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23012 AN: 151996 Hom.: 2340 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.144

GnomAD3 exomes AF: 0.0912 AC: 33 AN: 362 Hom.: 2 AF XY: 0.0891 AC XY: 18 AN XY: 202

Gnomad NFE exome AF: 0.0909

Gnomad OTH exome AF: 0.100

GnomAD4 exome AF: 0.142 AC: 313 AN: 2202 Hom.: 36 Cov.: 0 AF XY: 0.144 AC XY: 157 AN XY: 1094

Gnomad4 AFR exome AF: 0.243

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.149

Gnomad4 NFE exome AF: 0.0816

Gnomad4 OTH exome AF: 0.180

GnomAD4 genome AF: 0.151 AC: 23041 AN: 152114 Hom.: 2342 Cov.: 32 AF XY: 0.152 AC XY: 11332 AN XY: 74340

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0956

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0427 Hom.: 46

Bravo AF: 0.155

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57629257; hg19: chr16-70064261;