dbSNP rs6841938: MIR1255B1:n.3C>T (chr4-36426426-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000636325.1(MIR1255B1):n.3C>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 0.102 in 155,446 control chromosomes in the GnomAD database, including 988 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 0.10 ( 970 hom., cov: 33)

Exomes 𝑓: 0.093 ( 18 hom. )

Consequence

MIR1255B1
ENST00000636325.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

15 publications found

Variant links:

Genes affected

MIR1255B1 (HGNC:35366): (microRNA 1255b-1) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1255B1 links:

LINC02505 (HGNC:53494): (long intergenic non-protein coding RNA 2505)

LINC02505 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR1255B1	NR_031701.1 link	n.3C>T		non_coding_transcript_exon_variant	Exon 1 of 1
MIR1255B1	unassigned_transcript_744	n.1C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR1255B1	ENST00000636325.1 link	n.3C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02505	ENST00000733117.1 link	n.206-7666C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15578

AN:

152036

Hom.:

969

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.0732

Gnomad ASJ

AF:

0.0688

Gnomad EAS

AF:

0.0121

Gnomad SAS

AF:

0.0276

Gnomad FIN

AF:

0.0937

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0857

Gnomad OTH

AF:

0.0959

GnomAD2 exomes

AF:

0.0863

AC:

550

AN:

6372

AF XY:

0.0796

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.0806

Gnomad ASJ exome

AF:

0.0663

Gnomad EAS exome

AF:

0.0143

Gnomad FIN exome

AF:

0.500

Gnomad NFE exome

AF:

0.0856

Gnomad OTH exome

AF:

0.0676

GnomAD4 exome

AF:

0.0933

AC:

307

AN:

3292

Hom.:

Cov.:

AF XY:

0.0937

AC XY:

175

AN XY:

1868

show subpopulations

African (AFR)

AF:

0.174

AC:

AN:

American (AMR)

AF:

0.0357

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0242

AC:

AN:

124

European-Finnish (FIN)

AF:

0.0943

AC:

AN:

424

Middle Eastern (MID)

AF:

0.105

AC:

171

AN:

1634

European-Non Finnish (NFE)

AF:

0.0858

AC:

AN:

664

Other (OTH)

AF:

0.0856

AC:

AN:

222

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.102

AC:

15591

AN:

152154

Hom.:

970

Cov.:

AF XY:

0.0999

AC XY:

7436

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.165

AC:

6843

AN:

41500

American (AMR)

AF:

0.0732

AC:

1119

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0688

AC:

239

AN:

3472

East Asian (EAS)

AF:

0.0121

AC:

AN:

5190

South Asian (SAS)

AF:

0.0276

AC:

133

AN:

4814

European-Finnish (FIN)

AF:

0.0937

AC:

991

AN:

10578

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0857

AC:

5827

AN:

67996

Other (OTH)

AF:

0.0949

AC:

200

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

707

1414

2121

2828

3535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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:

0.101

Hom.:

108

Bravo

AF:

0.105

Asia WGS

AF:

0.0340

AC:

118

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

4.1

(source)

DANN

Benign

0.66

PhyloP100

-1.2

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

Computational scores

Splicing

Publications

Other links and lift over