Variant rs272867 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_110997.1(MIR3936HG):n.560+4451C>T 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 0.598 in 152,048 control chromosomes in the GnomAD database, including 27,742 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 0.60 ( 27742 hom., cov: 32)

Consequence

MIR3936HG
NR_110997.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.255

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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.560+4451C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR3936HG	ENST00000621103.4 linkuse as main transcript	n.560+4451C>T	intron_variant, non_coding_transcript_variant	1
MIR3936HG	ENST00000616965.1 linkuse as main transcript	n.343+4451C>T	intron_variant, non_coding_transcript_variant	5
MIR3936HG	ENST00000669845.1 linkuse as main transcript	n.187-10438C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

90793

AN:

151928

Hom.:

27713

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.761

Gnomad AMR

AF:

0.650

Gnomad ASJ

AF:

0.585

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.604

Gnomad OTH

AF:

0.612

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.598

AC:

90876

AN:

152048

Hom.:

27742

Cov.:

AF XY:

0.587

AC XY:

43617

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.655

Gnomad4 AMR

AF:

0.650

Gnomad4 ASJ

AF:

0.585

Gnomad4 EAS

AF:

0.331

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.488

Gnomad4 NFE

AF:

0.604

Gnomad4 OTH

AF:

0.612

Alfa

AF:

0.602

Hom.:

54095

Bravo

AF:

0.619

Asia WGS

AF:

0.383

AC:

1333

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

DANN

Benign

0.75

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over