Variant 5-132369574-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000457998.2(MIR3936HG):n.75C>G 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 0.318 in 184,386 control chromosomes in the GnomAD database, including 9,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 8146 hom., cov: 32)

Exomes 𝑓: 0.31 ( 1661 hom. )

Consequence

MIR3936HG
ENST00000457998.2 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.116

Variant links:

Genes affected

MIR3936HG (HGNC:):

MIR3936HG 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=-0.83).

BP6

Variant 5-132369574-G-C is Benign according to our data. Variant chr5-132369574-G-C is described in ClinVar as [Benign]. Clinvar id is 1221263.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3936HG	NR_110997.1 linkuse as main transcript	n.73+270C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR3936HG	ENST00000621103.4 linkuse as main transcript	n.73+270C>G	intron_variant		1
MIR3936HG	ENST00000457998.2 linkuse as main transcript	n.75C>G	non_coding_transcript_exon_variant	1/2	2
MIR3936HG	ENST00000649993.1 linkuse as main transcript	n.86C>G	non_coding_transcript_exon_variant	1/5

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48676

AN:

151904

Hom.:

8142

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.561

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.307

GnomAD4 exome

AF:

0.309

AC:

10002

AN:

32364

Hom.:

1661

Cov.:

AF XY:

0.306

AC XY:

5061

AN XY:

16528

show subpopulations

Gnomad4 AFR exome

AF:

0.270

Gnomad4 AMR exome

AF:

0.265

Gnomad4 ASJ exome

AF:

0.291

Gnomad4 EAS exome

AF:

0.346

Gnomad4 SAS exome

AF:

0.561

Gnomad4 FIN exome

AF:

0.407

Gnomad4 NFE exome

AF:

0.291

Gnomad4 OTH exome

AF:

0.320

GnomAD4 genome

AF:

0.320

AC:

48707

AN:

152022

Hom.:

8146

Cov.:

AF XY:

0.332

AC XY:

24630

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.284

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.302

Gnomad4 EAS

AF:

0.380

Gnomad4 SAS

AF:

0.562

Gnomad4 FIN

AF:

0.431

Gnomad4 NFE

AF:

0.312

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.214

Hom.:

535

Bravo

AF:

0.302

Asia WGS

AF:

0.477

AC:

1656

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.5

DANN

Benign

0.63

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