rs67780153

Positions:

• chr15-38985058-A-AGAG

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.174-10824_174-10823insCTC 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: 31)
• Consequence: ENSG00000259345 ENST00000560484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

ENSG00000259345 (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
LOC105370777	XR_007064586.1	n.1446-10824_1446-10823insCTC		intron_variant
LOC105370777	XR_007064587.1	n.1446-10824_1446-10823insCTC		intron_variant
LOC105370777	XR_007064588.1	n.624-10824_624-10823insCTC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000560197.5	n.171-10824_171-10823insCTC		intron_variant		5
ENSG00000259345	ENST00000560484.1	n.174-10824_174-10823insCTC		intron_variant		4
ENSG00000259345	ENST00000561058.5	n.231-10824_231-10823insCTC		intron_variant		4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

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: rs67780153; hg19: chr15-39277259;