Variant 7-129774734-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2

The NR_029512.1(MIR96):n.36T>C variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 474,422 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0031 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0034 ( 4 hom. )

Consequence

MIR96
NR_029512.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 8.60

Variant links:

Genes affected

MIR96 (HGNC:):

MIR96 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 7-129774734-A-G is Benign according to our data. Variant chr7-129774734-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 163977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-129774734-A-G is described in Lovd as [Benign].

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR96	NR_029512.1 linkuse as main transcript	n.36T>C	non_coding_transcript_exon_variant	1/1
MIR96	unassigned_transcript_1306 use as main transcript	n.-16T>C	upstream_gene_variant
MIR96	unassigned_transcript_1307 use as main transcript	n.*5T>C	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR96	ENST00000362288.1 linkuse as main transcript	n.36T>C		non_coding_transcript_exon_variant	1/1	6
ENSG00000286380	ENST00000710872.1 linkuse as main transcript	n.431+5056T>C		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00309

AC:

470

AN:

152086

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000851

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00565

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00521

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00295

AC:

477

AN:

161596

Hom.:

AF XY:

0.00283

AC XY:

241

AN XY:

85152

show subpopulations

Gnomad AFR exome

AF:

0.000531

Gnomad AMR exome

AF:

0.00140

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000955

Gnomad FIN exome

AF:

0.00601

Gnomad NFE exome

AF:

0.00494

Gnomad OTH exome

AF:

0.00176

GnomAD4 exome

AF:

0.00340

AC:

1095

AN:

322218

Hom.:

Cov.:

AF XY:

0.00317

AC XY:

577

AN XY:

181844

show subpopulations

Gnomad4 AFR exome

AF:

0.000662

Gnomad4 AMR exome

AF:

0.00135

Gnomad4 ASJ exome

AF:

0.0000925

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000734

Gnomad4 FIN exome

AF:

0.00530

Gnomad4 NFE exome

AF:

0.00511

Gnomad4 OTH exome

AF:

0.00290

GnomAD4 genome

AF:

0.00309

AC:

470

AN:

152204

Hom.:

Cov.:

AF XY:

0.00316

AC XY:

235

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.000939

Gnomad4 AMR

AF:

0.000850

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00565

Gnomad4 NFE

AF:

0.00521

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00395

Hom.:

Bravo

AF:

0.00250

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 22, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 15, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	MIR96: BS2 -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 05, 2013	36T>C in Exon 1 of MIR96: This variant is not expected to have clinical signific ance because it has been identified in 0.7% (5/725) of American European and Eur opean chromosomes by the 1000 Genome Project (http://www.1000genomes.org/; dbSNP rs41274239) as well as 0.4% (28/7102) of European American chromosomes from a b road population by the NHLBI Exome Sequencing Project (http://evs.gs.washington. edu/EVS/), and is not located in the seed region of the miRNA. -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 06, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

DANN

Benign

0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over