Genetic Variant MIR1915HG: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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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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR1915HG	NR_160800.1 link	n.1752C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MIR1915HG	ENST00000658000.1 link	n.1752C>A	non_coding_transcript_exon_variant	Exon 2 of 2
MIR1915HG	ENST00000701218.2 link	n.322+2045C>A	intron_variant	Intron 1 of 1
MIR1915HG	ENST00000830463.1 link	n.259+2045C>A	intron_variant	Intron 1 of 2
ENSG00000308071	ENST00000830852.1 link	n.110+322G>T	intron_variant	Intron 1 of 1

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over