9-35658019-A-ACGTCCTCAGCTTCGTCCTCAGCTT

Position:

• chr9-35658019-A-ACGTCCTCAGCTTCGTCCTCAGCTT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: -1.84

Genes affected

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 9-35658019-A-ACGTCCTCAGCTTCGTCCTCAGCTT is Pathogenic according to our data. Variant chr9-35658019-A-ACGTCCTCAGCTTCGTCCTCAGCTT is described in ClinVar as [Pathogenic]. Clinvar id is 14218.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35658019_35658020insCGTCCTCAGCTTCGTCCTCAGCTT		intergenic_region
RMRP	NR_003051.4	n.-1_1insAAGCTGAGGACGAAGCTGAGGACG		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMRP	ENST00000363046.1	n.-3_-2insAAGCTGAGGACGAAGCTGAGGACG		upstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 34

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Metaphyseal dysplasia without hypotrichosis Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Feb 01, 2002

- -

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: rs1554651400; hg19: chr9-35658016;