Genetic Variant MIRLET7BHG:n.3935C>T (chr22-46113303-C-T) – 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.3935C>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 0.568 in 182,778 control chromosomes in the GnomAD database, including 32,793 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 0.55 ( 25937 hom., cov: 34)

Exomes 𝑓: 0.66 ( 6856 hom. )

Consequence

MIRLET7BHG
ENST00000360737.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Publications

6 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
MIRLET7BHG	NR_027033.2 link	n.4092C>T	non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	NR_110479.1 link	n.3941C>T	non_coding_transcript_exon_variant	Exon 5 of 5
LOC124905135	XM_047441694.1 link	c.*8714C>T	3_prime_UTR_variant	Exon 2 of 2	XP_047297650.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIRLET7BHG	ENST00000360737.4 link	n.3935C>T	non_coding_transcript_exon_variant	Exon 5 of 5	2
MIRLET7BHG	ENST00000794300.1 link	n.1163C>T	non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	ENST00000794301.1 link	n.1044C>T	non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

83697

AN:

152052

Hom.:

25914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.572

Gnomad AMR

AF:

0.632

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.973

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.639

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.642

Gnomad OTH

AF:

0.599

GnomAD4 exome

AF:

0.657

AC:

20120

AN:

30608

Hom.:

6856

Cov.:

AF XY:

0.661

AC XY:

10805

AN XY:

16346

show subpopulations

African (AFR)

AF:

0.252

AC:

125

AN:

496

American (AMR)

AF:

0.664

AC:

1831

AN:

2758

Ashkenazi Jewish (ASJ)

AF:

0.705

AC:

444

AN:

630

East Asian (EAS)

AF:

0.973

AC:

1035

AN:

1064

South Asian (SAS)

AF:

0.690

AC:

3317

AN:

4804

European-Finnish (FIN)

AF:

0.655

AC:

783

AN:

1196

Middle Eastern (MID)

AF:

0.675

AC:

AN:

120

European-Non Finnish (NFE)

AF:

0.640

AC:

11500

AN:

17964

Other (OTH)

AF:

0.637

AC:

1004

AN:

1576

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

323

646

969

1292

1615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

252

378

504

630

<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:

0.550

AC:

83747

AN:

152170

Hom.:

25937

Cov.:

AF XY:

0.556

AC XY:

41327

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.263

AC:

10910

AN:

41538

American (AMR)

AF:

0.633

AC:

9680

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2381

AN:

3472

East Asian (EAS)

AF:

0.973

AC:

5019

AN:

5158

South Asian (SAS)

AF:

0.698

AC:

3369

AN:

4830

European-Finnish (FIN)

AF:

0.639

AC:

6762

AN:

10586

Middle Eastern (MID)

AF:

0.619

AC:

182

AN:

294

European-Non Finnish (NFE)

AF:

0.642

AC:

43646

AN:

67974

Other (OTH)

AF:

0.605

AC:

1276

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1666

3332

4999

6665

8331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<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:

0.491

Hom.:

2659

Bravo

AF:

0.541

Asia WGS

AF:

0.780

AC:

2712

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.9

(source)

DANN

Benign

0.45

PhyloP100

-0.072

Mutation Taster

=100/0

polymorphism (auto)

(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