dbSNP rs947893: MIR100HG:n.76-72T>C (chr11-122091791-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000524376.2(MIR100HG):n.76-72T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,018 control chromosomes in the GnomAD database, including 8,932 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 0.34 ( 8931 hom., cov: 32)

Exomes 𝑓: 0.75 ( 1 hom. )

Consequence

MIR100HG
ENST00000524376.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.284

Variant links:

Genes affected

MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]

MIR100HG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR100HG	NR_024430.2 link	n.492-51T>C	intron_variant	Intron 3 of 3
MIR100HG	NR_137175.1 link	n.784-72T>C	intron_variant	Intron 1 of 1
MIR100HG	NR_137176.1 link	n.474-51T>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR100HG	ENST00000524376.2 link	n.76-72T>C	intron_variant	Intron 1 of 1	1
MIR100HG	ENST00000528986.2 link	n.897-51T>C	intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000534782.4 link	n.388-72T>C	intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes

AF:

0.343

AC:

52110

AN:

151896

Hom.:

8925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.321

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.340

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.359

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.750

GnomAD4 genome

AF:

0.343

AC:

52149

AN:

152014

Hom.:

8931

Cov.:

AF XY:

0.340

AC XY:

25281

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.326

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.277

Gnomad4 EAS

AF:

0.321

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.340

Gnomad4 NFE

AF:

0.363

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.360

Hom.:

1233

Bravo

AF:

0.344

Asia WGS

AF:

0.329

AC:

1145

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.82

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