5-160477722-T-C

Variant names:

• chr5-160477722-T-C
• rs883517
• ENST00000517927.2:n.311-7577T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000517927.2(MIR3142HG):​n.311-7577T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,970 control chromosomes in the GnomAD database, including 4,565 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 0.21 (4565 hom., cov: 32)
• Consequence: MIR3142HG ENST00000517927.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939
• Publications: 6 publications found

Genes affected

MIR3142HG (HGNC:51944): (MIR3142 host gene)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3142HG	NR_132748.1	n.191-7577T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000517927.2	n.311-7577T>C		intron_variant	Intron 1 of 1	1
MIR3142HG	ENST00000642173.1	n.77-7577T>C		intron_variant	Intron 1 of 1
MIR3142HG	ENST00000770454.1	n.536+9282T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32583 AN: 151852 Hom.: 4552 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.215 AC: 32627 AN: 151970 Hom.: 4565 Cov.: 32 AF XY: 0.214 AC XY: 15867 AN XY: 74288

African (AFR) AF: 0.386 AC: 15977 AN: 41424

American (AMR) AF: 0.211 AC: 3223 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1944 AN: 5164

South Asian (SAS) AF: 0.188 AC: 903 AN: 4810

European-Finnish (FIN) AF: 0.108 AC: 1137 AN: 10574

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8539 AN: 67968

Other (OTH) AF: 0.217 AC: 456 AN: 2102

Alfa AF: 0.160 Hom.: 6191

Bravo AF: 0.231

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.90
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs883517; hg19: chr5-159904729;