dbSNP rs2277920: MIR3142HG:n.310+258T>C (chr5-160468698-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000517927.2(MIR3142HG):n.310+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
ENST00000517927.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193

Publications

1 publications found

Variant links:

Genes affected

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

MIR3142HG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	n.190+258T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR3142HG	ENST00000517927.2 link	n.310+258T>C	intron_variant	Intron 1 of 1	1
MIR3142HG	ENST00000642173.1 link	n.77-16601T>C	intron_variant	Intron 1 of 1
MIR3142HG	ENST00000770454.1 link	n.536+258T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0757

AC:

11447

AN:

151238

Hom.:

678

Cov.:

show subpopulations

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.:

AF XY:

0.0782

AC XY:

5780

AN XY:

73942

show subpopulations

African (AFR)

AF:

0.143

AC:

5916

AN:

41320

American (AMR)

AF:

0.104

AC:

1582

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.0133

AC:

AN:

3460

East Asian (EAS)

AF:

0.189

AC:

963

AN:

5092

South Asian (SAS)

AF:

0.123

AC:

583

AN:

4756

European-Finnish (FIN)

AF:

0.0367

AC:

381

AN:

10382

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0271

AC:

1836

AN:

67808

Other (OTH)

AF:

0.0773

AC:

163

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

493

986

1478

1971

2464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0541

Hom.:

145

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

(source)

DANN

Benign

0.76

PhyloP100

0.19

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over