Genetic Variant ENST00000658000.1:n.1752C>A (chr10-21494705-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000658000.1(MIR1915HG):n.1752C>A 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 0.0000511 in 19,586 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)

Exomes 𝑓: 0.000051 ( 0 hom. )

Consequence

MIR1915HG
ENST00000658000.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

0 publications found

Variant links:

Genes affected

MIR1915HG (HGNC:31448): (MIR1915 host gene)

MIR1915HG links:

ENSG00000308071 (HGNC:):

ENSG00000308071 links:

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new If you want to explore the variant's impact on the transcript ENST00000658000.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658000.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1915HG	NR_160800.1		n.1752C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MIR1915HG	ENST00000658000.1	n.1752C>A	non_coding_transcript_exon	Exon 2 of 2
MIR1915HG	ENST00000701218.2	n.322+2045C>A	intron	N/A
MIR1915HG	ENST00000830463.1	n.259+2045C>A	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000511

AC:

AN:

19586

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

10266

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

404

American (AMR)

AF:

0.00

AC:

AN:

394

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

500

East Asian (EAS)

AF:

0.00

AC:

AN:

2340

South Asian (SAS)

AF:

0.00

AC:

AN:

136

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000839

AC:

AN:

11920

Other (OTH)

AF:

0.00

AC:

AN:

1008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

-0.0070

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over