Variant rs2631368 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_110997.1(MIR3936HG):n.73+239A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 212,720 control chromosomes in the GnomAD database, including 11,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 8122 hom., cov: 33)

Exomes 𝑓: 0.32 ( 3151 hom. )

Consequence

MIR3936HG
NR_110997.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.35

Variant links:

Genes affected

MIR3936HG (HGNC:40538): (MIR3936 host gene)

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=-0.81).

BP6

Variant 5-132369605-T-G is Benign according to our data. Variant chr5-132369605-T-G is described in ClinVar as [Benign]. Clinvar id is 1266598.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	UniProt
MIR3936HG	NR_110997.1 linkuse as main transcript	n.73+239A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3936HG	ENST00000621103.4 linkuse as main transcript	n.73+239A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48627

AN:

151904

Hom.:

8118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.561

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.312

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.316

AC:

19153

AN:

60698

Hom.:

3151

Cov.:

AF XY:

0.312

AC XY:

9673

AN XY:

30972

show subpopulations

Gnomad4 AFR exome

AF:

0.278

Gnomad4 AMR exome

AF:

0.284

Gnomad4 ASJ exome

AF:

0.299

Gnomad4 EAS exome

AF:

0.356

Gnomad4 SAS exome

AF:

0.559

Gnomad4 FIN exome

AF:

0.416

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.320

AC:

48658

AN:

152022

Hom.:

8122

Cov.:

AF XY:

0.331

AC XY:

24613

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.284

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.302

Gnomad4 EAS

AF:

0.379

Gnomad4 SAS

AF:

0.562

Gnomad4 FIN

AF:

0.429

Gnomad4 NFE

AF:

0.312

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.323

Hom.:

1277

Bravo

AF:

0.302

Asia WGS

AF:

0.476

AC:

1654

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

-0.81

CADD

Benign

0.77

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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