rs2277920

Variant names:

• chr5-160468698-T-C
• rs2277920
• ENST00000517927.1:n.173+258T>C

Variant summary

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

The ENST00000517927.1(MIR3142HG):​n.173+258T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 151,356 control chromosomes in the GnomAD database, including 682 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 0.076 (682 hom., cov: 32)
• Consequence: MIR3142HG ENST00000517927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3142HG	NR_132748.1	n.190+258T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000517927.1	n.173+258T>C		intron_variant	Intron 1 of 1	1
MIR3142HG	ENST00000642173.1	n.77-16601T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11447 AN: 151238 Hom.: 678 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0758 AC: 11477 AN: 151356 Hom.: 682 Cov.: 32 AF XY: 0.0782 AC XY: 5780 AN XY: 73942

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0367

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0548 Hom.: 123

Bravo AF: 0.0838

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2277920; hg19: chr5-159895705;