rs2910164

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_029701(MIR146A):n.60C>G 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 0.702 in 151942 control chromosomes in the gnomAD Genomes database, including 38071 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 0.70 ( 38071 hom., cov: 31)

Exomes 𝑓: 0.71 ( 64108 hom. )

Consequence

MIR146A
NR_029701 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57

Links

MIR3142HG (HGNC:51944):

MIR146A (HGNC:31533):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR146A	NR_029701.1 linkuse as main transcript	n.60C>G		non_coding_transcript_exon_variant	1/1
MIR3142HG	NR_132748.1 linkuse as main transcript	n.303C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR3142HG	ENST00000517927.1 linkuse as main transcript	n.286C>G	non_coding_transcript_exon_variant	2/2	1
MIR3142HG	ENST00000642173.1 linkuse as main transcript	n.189C>G	non_coding_transcript_exon_variant	2/2
MIR146A	ENST00000385201.1 linkuse as main transcript	n.60C>G	mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

106630

AN:

151942

Hom.:

38071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.766

Gnomad OTH

AF:

0.687

GnomAD3 exomes

AF:

0.713

AC:

175623

AN:

246292

Hom.:

64108

AF XY:

0.719

AC XY:

95733

AN XY:

133108

show subpopulations

Gnomad AFR exome

AF:

0.598

Gnomad AMR exome

AF:

0.694

Gnomad ASJ exome

AF:

0.777

Gnomad EAS exome

AF:

0.372

Gnomad SAS exome

AF:

0.720

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.770

Gnomad OTH exome

AF:

0.730

GnomAD4 exome

AF:

0.737

AC:

277348

AN:

376330

Hom.:

103685

AF XY:

0.738

AC XY:

157630

AN XY:

213566

show subpopulations

Gnomad4 AFR exome

AF:

0.599

Gnomad4 AMR exome

AF:

0.694

Gnomad4 ASJ exome

AF:

0.777

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.727

Gnomad4 FIN exome

AF:

0.782

Gnomad4 NFE exome

AF:

0.772

Gnomad4 OTH exome

AF:

0.733

Alfa

AF:

0.755

Hom.:

14093

Bravo

AF:

0.691

Asia WGS

AF:

0.549

AC:

1913

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

Cadd

Benign

Dann

Benign

0.76

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over