Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000436880.2(MIR181A1HG):n.1819C>T 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 0.724 in 151,930 control chromosomes in the GnomAD database, including 40,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 40351 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

MIR181A1HG
ENST00000436880.2 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts P:1B:2

Conservation

PhyloP100: -0.819

Publications

2 publications found

Variant links:

Genes affected

MIR181A1HG (HGNC:48659): (MIR181A1 host gene)

MIR181A1HG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-198898955-G-A is Benign according to our data. Variant chr1-198898955-G-A is described in ClinVar as Benign. ClinVar VariationId is 427755.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436880.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR181A1HG	NR_040073.1		n.363+1456C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR181A1HG	ENST00000436880.2	TSL:1	n.1819C>T	non_coding_transcript_exon	Exon 2 of 2
MIR181A1HG	ENST00000665868.3		n.1953C>T	non_coding_transcript_exon	Exon 2 of 2
MIR181A1HG	ENST00000432296.2	TSL:3	n.363+1456C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.724

AC:

109963

AN:

151812

Hom.:

40313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.822

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.750

Gnomad ASJ

AF:

0.778

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.874

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.650

Gnomad OTH

AF:

0.702

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.724

AC:

110059

AN:

151930

Hom.:

40351

Cov.:

AF XY:

0.730

AC XY:

54176

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.822

AC:

34088

AN:

41478

American (AMR)

AF:

0.751

AC:

11451

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.778

AC:

2698

AN:

3470

East Asian (EAS)

AF:

0.792

AC:

4070

AN:

5140

South Asian (SAS)

AF:

0.874

AC:

4220

AN:

4828

European-Finnish (FIN)

AF:

0.683

AC:

7199

AN:

10542

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.650

AC:

44124

AN:

67906

Other (OTH)

AF:

0.704

AC:

1485

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1512

3024

4536

6048

7560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<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:

0.700

Hom.:

4840

Bravo

AF:

0.728

Asia WGS

AF:

0.831

AC:

2884

AN:

3470

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Acute myeloblastic leukemia with maturation (1)

not provided (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.9

(source)

DANN

Benign

0.66

PhyloP100

-0.82

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over