Variant rs12587505 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NR_148991.1(MIR3171HG):n.253+142147T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)

Consequence

MIR3171HG
NR_148991.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.285

Variant links:

Genes affected

MIR3171HG (HGNC:56193): (MIR3171 host gene)

MIR3171HG links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3171HG	NR_148991.1 linkuse as main transcript	n.253+142147T>G		intron_variant, non_coding_transcript_variant
MIR3171HG	NR_148992.1 linkuse as main transcript	n.358+142042T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR3171HG	ENST00000555797.1 linkuse as main transcript	n.348+142147T>G	intron_variant, non_coding_transcript_variant	3
MIR3171HG	ENST00000556890.1 linkuse as main transcript	n.358+142042T>G	intron_variant, non_coding_transcript_variant	1
MIR3171HG	ENST00000553392.5 linkuse as main transcript	n.262+142147T>G	intron_variant, non_coding_transcript_variant	3
MIR3171HG	ENST00000554904.5 linkuse as main transcript	n.253+142147T>G	intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.5

DANN

Benign

0.63

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