dbSNP rs60639710: MIR181A1HG:n.2225C>A (chr1-198898549-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The ENST00000436880.2(MIR181A1HG):n.2225C>A 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 151,810 control chromosomes in the GnomAD database, including 40,262 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 40262 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: -0.376

Publications

2 publications found

Variant links:

Genes affected

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

MIR181A1HG links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000436880.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.8).

BP6

Variant 1-198898549-G-T is Benign according to our data. Variant chr1-198898549-G-T is described in ClinVar as Benign. ClinVar VariationId is 427754.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR181A1HG	NR_040073.1		n.363+1862C>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR181A1HG	ENST00000436880.2	TSL:1	n.2225C>A	non_coding_transcript_exon	Exon 2 of 2
MIR181A1HG	ENST00000653207.2		n.463C>A	non_coding_transcript_exon	Exon 3 of 3
MIR181A1HG	ENST00000665868.3		n.2359C>A	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.724

AC:

109832

AN:

151692

Hom.:

40228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.820

Gnomad AMI

AF:

0.562

Gnomad AMR

AF:

0.750

Gnomad ASJ

AF:

0.777

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.876

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.650

Gnomad OTH

AF:

0.701

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:

109921

AN:

151810

Hom.:

40262

Cov.:

AF XY:

0.730

AC XY:

54122

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.820

AC:

34019

AN:

41508

American (AMR)

AF:

0.750

AC:

11427

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.777

AC:

2699

AN:

3472

East Asian (EAS)

AF:

0.792

AC:

4076

AN:

5148

South Asian (SAS)

AF:

0.876

AC:

4221

AN:

4820

European-Finnish (FIN)

AF:

0.686

AC:

7199

AN:

10498

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.650

AC:

44078

AN:

67824

Other (OTH)

AF:

0.702

AC:

1480

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1519

3038

4557

6076

7595

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:

0.681

Hom.:

50364

Bravo

AF:

0.727

Asia WGS

AF:

0.829

AC:

2857

AN:

3448

ClinVar

ClinVar submissions

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

-0.80

CADD

Benign

8.7

(source)

DANN

Benign

0.71

PhyloP100

-0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over