20-290584-T-TTTTTAA

Position:

• chr20-290584-T-TTTTTAA

Variant summary

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

The NM_080571.2(C20orf96):​c.17+2_17+3insTTAAAA variant causes a splice donor, 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: 0)
• Consequence: C20orf96 NM_080571.2 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

C20orf96 (HGNC:16227): (chromosome 20 open reading frame 96)

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
C20orf96	NM_153269.3	c.20+6_20+7insTTAAAA		splice_region_variant, intron_variant		ENST00000360321.7	NP_695001.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C20orf96	ENST00000360321.7	c.20+6_20+7insTTAAAA		splice_region_variant, intron_variant		1	NM_153269.3	ENSP00000353470.2
C20orf96	ENST00000400269.4	c.17+2_17+3insTTAAAA		splice_donor_variant, intron_variant		1		ENSP00000383128.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 0

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: rs3835237; hg19: chr20-271225;