Variant 2-12190273-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_110196.1(MIR3681HG):n.327+23418G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,904 control chromosomes in the GnomAD database, including 1,831 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 0.11 ( 1831 hom., cov: 31)

Consequence

MIR3681HG
NR_110196.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.358

Variant links:

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 host gene)

MIR3681HG links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR3681HG	NR_110196.1 linkuse as main transcript	n.327+23418G>A	intron_variant, non_coding_transcript_variant
LOC105373432	XR_922806.2 linkuse as main transcript	n.368-479C>T	intron_variant, non_coding_transcript_variant
LOC105373432	XR_922807.2 linkuse as main transcript	n.279-479C>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR3681HG	ENST00000412294.5 linkuse as main transcript	n.315+23418G>A	intron_variant, non_coding_transcript_variant	2
	ENST00000701120.1 linkuse as main transcript	n.390-479C>T	intron_variant, non_coding_transcript_variant
MIR3681HG	ENST00000438292.5 linkuse as main transcript	n.246+23418G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17158

AN:

151786

Hom.:

1823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0421

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.234

Gnomad ASJ

AF:

0.0648

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.400

Gnomad FIN

AF:

0.0807

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0909

Gnomad OTH

AF:

0.122

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

GnomAD4 genome

AF:

0.113

AC:

17191

AN:

151904

Hom.:

1831

Cov.:

AF XY:

0.123

AC XY:

9169

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.0424

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.0648

Gnomad4 EAS

AF:

0.460

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.0807

Gnomad4 NFE

AF:

0.0909

Gnomad4 OTH

AF:

0.126

Alfa

AF:

0.111

Hom.:

687

Bravo

AF:

0.119

Asia WGS

AF:

0.418

AC:

1452

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.57

Splicing

Find out detailed SpliceAI scores 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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over