dbSNP rs738559: MIRLET7BHG:n.3864G>A (chr22-46113232-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 ENST00000360737.4(MIRLET7BHG):n.3864G>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 0.0367 in 179,072 control chromosomes in the GnomAD database, including 180 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 0.037 ( 138 hom., cov: 33)

Exomes 𝑓: 0.038 ( 42 hom. )

Consequence

MIRLET7BHG
ENST00000360737.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.906

Publications

4 publications found

Variant links:

Genes affected

MIRLET7BHG (HGNC:37189): (MIRLET7B host gene)

MIRLET7BHG links:

LOC124905135 (HGNC:):

LOC124905135 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
MIRLET7BHG	NR_027033.2 link	n.4021G>A	non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	NR_110479.1 link	n.3870G>A	non_coding_transcript_exon_variant	Exon 5 of 5
LOC124905135	XM_047441694.1 link	c.*8643G>A	3_prime_UTR_variant	Exon 2 of 2	XP_047297650.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIRLET7BHG	ENST00000360737.4 link	n.3864G>A	non_coding_transcript_exon_variant	Exon 5 of 5	2
MIRLET7BHG	ENST00000794300.1 link	n.1092G>A	non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	ENST00000794301.1 link	n.973G>A	non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.0366

AC:

5572

AN:

152218

Hom.:

138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.0857

Gnomad AMR

AF:

0.0591

Gnomad ASJ

AF:

0.0147

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0198

Gnomad FIN

AF:

0.0395

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0517

Gnomad OTH

AF:

0.0321

GnomAD4 exome

AF:

0.0379

AC:

1012

AN:

26736

Hom.:

Cov.:

AF XY:

0.0352

AC XY:

500

AN XY:

14208

show subpopulations

African (AFR)

AF:

0.00701

AC:

AN:

428

American (AMR)

AF:

0.0720

AC:

186

AN:

2584

Ashkenazi Jewish (ASJ)

AF:

0.0125

AC:

AN:

562

East Asian (EAS)

AF:

0.00

AC:

AN:

976

South Asian (SAS)

AF:

0.0169

AC:

AN:

3976

European-Finnish (FIN)

AF:

0.0326

AC:

AN:

1042

Middle Eastern (MID)

AF:

0.00781

AC:

AN:

128

European-Non Finnish (NFE)

AF:

0.0434

AC:

680

AN:

15658

Other (OTH)

AF:

0.0246

AC:

AN:

1382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

134

178

223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0366

AC:

5568

AN:

152336

Hom.:

138

Cov.:

AF XY:

0.0354

AC XY:

2641

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.0105

AC:

437

AN:

41582

American (AMR)

AF:

0.0588

AC:

900

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0147

AC:

AN:

3472

East Asian (EAS)

AF:

0.000386

AC:

AN:

5182

South Asian (SAS)

AF:

0.0199

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.0395

AC:

420

AN:

10622

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0517

AC:

3516

AN:

68022

Other (OTH)

AF:

0.0308

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

287

573

860

1146

1433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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:

0.0389

Hom.:

Bravo

AF:

0.0382

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

(source)

DANN

Benign

0.81

PhyloP100

-0.91

Mutation Taster

=100/0

polymorphism

(source)

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