chr16-70030358-C-T

Variant names:

• chr16-70030358-C-T
• rs57629257
• ENST00000531894.5:n.899+630G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

PDXDC2P-NPIPB14P (HGNC:53158): (PDXDC2P-NPIPB14P readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription between two pseudogenes, PDXDC2P (pyridoxal dependent decarboxylase domain containing 2, pseudogene) and NPIPB14P (nuclear pore complex interacting protein family, member B14, pseudogene). The individual pseudogene loci are not curated as transcribed regions. Readthrough transcripts likely do not encode functional proteins. [provided by RefSeq, Feb 2017]

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_036265.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1972-2	NR_036265.1		n.13C>T		non_coding_transcript_exon	Exon 1 of 1
	PDXDC2P-NPIPB14P	NR_003610.1		n.899+630G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDXDC2P-NPIPB14P	ENST00000531894.5	TSL:1	n.899+630G>A		intron	N/A
	MIR1972-2	ENST00000458813.1	TSL:6	n.13C>T		non_coding_transcript_exon	Exon 1 of 1
	PDXDC2P-NPIPB14P	ENST00000529089.1	TSL:2	n.769+630G>A		intron	N/A

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

GnomAD2 exomes AF: 0.0912 AC: 33 AN: 362 AF XY: 0.0891

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

African (AFR) AF: 0.243 AC: 18 AN: 74

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.149 AC: 14 AN: 94

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.140 AC: 229 AN: 1632

European-Non Finnish (NFE) AF: 0.0816 AC: 16 AN: 196

Other (OTH) AF: 0.180 AC: 35 AN: 194

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

African (AFR) AF: 0.259 AC: 10752 AN: 41470

American (AMR) AF: 0.0767 AC: 1174 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2072 AN: 5164

South Asian (SAS) AF: 0.142 AC: 683 AN: 4822

European-Finnish (FIN) AF: 0.0956 AC: 1010 AN: 10560

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0947 AC: 6439 AN: 68016

Other (OTH) AF: 0.147 AC: 310 AN: 2110

Alfa AF: 0.0391 Hom.: 46

Bravo AF: 0.155

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.66
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs57629257; hg19: chr16-70064261;