dbSNP rs9660525: MIR181A1HG:n.633G>T (chr1-198807802-C-A) – 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 ENST00000412162.1(MIR181A1HG):n.633G>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 0.393 in 152,026 control chromosomes in the GnomAD database, including 12,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 12186 hom., cov: 32)

Exomes 𝑓: 0.45 ( 3 hom. )

Consequence

MIR181A1HG
ENST00000412162.1 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.658

Publications

3 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 ENST00000412162.1, 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=-0.95).

BP6

Variant 1-198807802-C-A is Benign according to our data. Variant chr1-198807802-C-A is described in ClinVar as Benign. ClinVar VariationId is 427752.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412162.1. 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.*201G>T		downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR181A1HG	ENST00000412162.1	TSL:3	n.633G>T	non_coding_transcript_exon	Exon 2 of 2
MIR181A1HG	ENST00000432296.2	TSL:3	n.805G>T	non_coding_transcript_exon	Exon 3 of 3
MIR181A1HG	ENST00000660348.1		n.356-28499G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59645

AN:

151886

Hom.:

12165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.573

Gnomad SAS

AF:

0.599

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.401

GnomAD4 exome

AF:

0.455

AC:

AN:

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

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)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.393

AC:

59707

AN:

152004

Hom.:

12186

Cov.:

AF XY:

0.402

AC XY:

29885

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.299

AC:

12374

AN:

41402

American (AMR)

AF:

0.489

AC:

7470

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.433

AC:

1503

AN:

3470

East Asian (EAS)

AF:

0.572

AC:

2955

AN:

5162

South Asian (SAS)

AF:

0.600

AC:

2890

AN:

4820

European-Finnish (FIN)

AF:

0.428

AC:

4528

AN:

10568

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.394

AC:

26799

AN:

67980

Other (OTH)

AF:

0.402

AC:

850

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1828

3656

5485

7313

9141

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<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:

0.385

Hom.:

4092

Bravo

AF:

0.389

Asia WGS

AF:

0.540

AC:

1876

AN:

3478

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

-0.95

CADD

Benign

3.6

(source)

DANN

Benign

0.35

PhyloP100

0.66

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over