rs35027589

Positions:

• chrX-147213546-T-TC

Variant summary

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

The NR_030231.1(MIR513A1):​n.45dupG variant causes a non coding transcript exon 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: 23)
• Consequence: MIR513A1 NR_030231.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

MIR513A1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR513A1	NR_030231.1	n.45dupG		non_coding_transcript_exon_variant	1/1
MIR513A1	unassigned_transcript_3848	n.9dupG		non_coding_transcript_exon_variant	1/1
LOC105373347	XR_005647083.2	n.133-4671dupC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR513A1	ENST00000385138.1	n.45dupG		non_coding_transcript_exon_variant	1/1	6
ENSG00000284377	ENST00000639829.1	n.179-4671dupC		intron_variant		5
ENSG00000284377	ENST00000701574.1	n.130-4671dupC		intron_variant

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35027589; hg19: chrX-146295064;