Variant rs34864809 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The XM_047449437.1(LOC112267908):c.693+23713dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

LOC112267908
XM_047449437.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0680

Variant links:

Genes affected

LOC112267908 (HGNC:):

LOC112267908 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein
LOC112267908	XM_047449437.1 linkuse as main transcript	c.693+23713dupG	intron_variant		XP_047305393.1
MIR548I1	NR_031687.1 linkuse as main transcript	n.24dupC	non_coding_transcript_exon_variant	1/1
LOC105374312	NR_153417.1 linkuse as main transcript	n.195-7244dupG	intron_variant
MIR548I1	unassigned_transcript_675 use as main transcript	n.-15dupC	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR548I1	ENST00000408810.1 linkuse as main transcript	n.24dupC	non_coding_transcript_exon_variant	1/1	6
ENSG00000272840	ENST00000610060.1 linkuse as main transcript	n.195-7244dupG	intron_variant		3
ENSG00000284624	ENST00000641586.1 linkuse as main transcript	n.171+23713dupG	intron_variant
ENSG00000284624	ENST00000641650.1 linkuse as main transcript	n.303+23713dupG	intron_variant

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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