rs34557733

Positions:

• chr14-101026792-G-GA

Variant summary

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

The XM_047432049.1(LOC124903407):​c.*5990dupA variant causes a 3 prime UTR 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: LOC124903407 XM_047432049.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.15

Genes affected

LOC124903407 (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
LOC124903407	XM_047432049.1	c.*5990dupA		3_prime_UTR_variant	5/5		XP_047288005.1
MIR329-1	NR_029967.1	n.10dupA		non_coding_transcript_exon_variant	1/1
MIR329-1	unassigned_transcript_2389	n.-5_-4insA		upstream_gene_variant
MIR329-1	unassigned_transcript_2390	n.-42_-41insA		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR329-1	ENST00000385028.3	n.10dupA		non_coding_transcript_exon_variant	1/1	6
MEG8	ENST00000636391.2	n.2086-552dupA		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

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: rs34557733; hg19: chr14-101493129;