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

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 CliVar as Benign. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR181A1HG	NR_040073.1 link	n.*201G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR181A1HG	ENST00000412162.1 link	n.633G>T	non_coding_transcript_exon_variant	Exon 2 of 2	3
MIR181A1HG	ENST00000432296.2 link	n.805G>T	non_coding_transcript_exon_variant	Exon 3 of 3	3
MIR181A1HG	ENST00000660348.1 link	n.356-28499G>T	intron_variant	Intron 2 of 2

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

Significance: Benign

Submissions summary: Pathogenic:1Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Acute myeloblastic leukemia with maturation

Pathogenic:1

Fujian Institute of Hematology, Fujian Medical University

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:case-control

This variant contributes to development of AML-M2 -

not specified

Benign:1

Oct 28, 2020

H3Africa Consortium

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:research

While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.188, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over